Life As A Shadow
by Annelantis
Summary: Set after series finale. Elizabeth Weir is floating in space. She is visited by an old friend who offers her a chance to save herself from the fate she has chosen. John Sheppard is back on Earth and contemplating how he can continue without the woman he loves. He then makes a decision that could change the lives of those around him forever.
1. Chapter 1

A/N: So this has been fermenting in my brain for about three years now. But a rewatch of the entire Series made me decide to actually put pen to paper. I was also inspired by this website which I only discovered a few months ago. If only I had known about it years ago.

Anyway, I have never posted a story before so I am a bit nervous. Please review and let me know what you think. I shall hopefully be posting one chapter a week. Just to warn you, I am very much into Sparky and miss it a lot.

DISCLAIMER: I do not own the characters or the premise or anything else that is to do with Stargate: Atlantis. If only I did. This story, however, is my own. There will be some flashbacks to scenes from episodes so credit for these goes to the writers, etc.

P.S. Thanks to my husband for reading each chapter and encouraging me to take this step.

PART ONE

Chapter 1

Christmas. It was her favourite day of the year when she was a girl. The anticipation, the inability to sleep, the urge to sneak downstairs to see if Santa had eaten the cookies she had made for him. Even as she got older and internally questioned the logistics - how a team of flying reindeer could take one sleigh with one rather rotund man and a sack full of gifts and deliver presents to all the children in all the world in one night - she lay in her bed looking up at the ceiling, too excited to sleep.

Every Christmas, her mother and father would take her and her brother to the cabin by the lake, just a few miles outside of Vancouver. Being in Canada always guaranteed a white Christmas. Christmas morning was spent opening presents by a roaring fireplace, followed by wrapping up snugly in big coats, woolly hats and gloves and venturing out into the winter wonderland to build a snow family and get into vigorous snowball fights with her brother. They would then run inside for the extraordinarily warm hot chocolate that Mom made for them, drinking and talking with Mom and Dad whilst sitting on the rug in front of the fireplace.

Christmas dinner was always an illustrious affair. Mom and Dad worked together to make sure everything came together perfectly. She ate and ate until she was sure she would burst. But she was always tinged with regret that she couldn't eat just a little bit more.

The evening was spent relaxing by the fire. Mom and Dad fell asleep on the sofa while she played with her new toys. The exception was the year she had received a telescope. Dad set it up for her on the cabin porch and she studied the constellations for hours, imagining stars surrounded by planets and visiting each one. She was so sure when she was nine that she was going to be an astronaut.

She cringed as she recalled going to the cabin when she was fifteen. She had argued with Mom that she wanted to stay home in Washington D.C. She wanted to see her friends and she couldn't imagine spending days away from Jordan, the love of her life. Of course, nothing had ever happened between them - she had been too afraid to tell him how she felt. But being without him would have been like being without oxygen. So she had used all her highly honed skills to negotiate staying behind. Her arguments had seemed logical and rational. When Mom had still said no, reason went out the window and she shouted, begged and cried. She had sulked the entire way there and spent most of her time lying on her bed or sitting out on the porch, allowing the cold air to chill her to the bone.

Thinking back, she much preferred to remember Christmas when she was a child. They were the best Christmases, her favourite one of course being the year she spent the night stargazing.

Until now. She had been led to this destination by the hand, unable to see where she was being taken thanks to the blindfold. The hand that led her was warm and she felt the tingles up her spine that always came when he touched her. She wondered when that would stop. Her stomach was filled with the anticipatory butterflies she had not felt since those Christmas days in Canada. How was it that he could make her feel this way again?

She nearly collided into him, so lost in her thoughts that she had not realised he had stopped. She felt her cheeks heat up in a blush. "Sorry," she said.

He moved around behind her and she felt his fingers in her hair as he untied the blindfold. Just before removing it though, he leaned forward and whispered in her ear, "Ready?"

She shivered slightly and nodded. The blindfold came away from her eyes and she gasped. The Gate Room and Control Room had been beautifully decorated. The control consoles were covered with white sheets and two large snowman figures (wearing the uniform jackets of the Atlantis staff - one in dark grey and blue, the other in dark grey and red) sitting behind them. White confetti covered the floor and the stairs leading down to the Gate Room, perhaps to emulate snow. In front of the Stargate, on the raised platform was a table. The centrepiece of the table was a small, colourfully lit Christmas tree. Surrounding the tree was dinner with all the traditional trappings she remembered: a roast turkey, roast potatoes, mashed potatoes, a myriad of different vegetables, cranberry sauce and gravy. A glass of wine was at each table setting.

Sitting around the table were the people she would want to spend her time with in a galaxy far from her family. Teyla looked beautiful in her blue Athosian dress, finished off with gold tinsel around her neck like a scarf. Ronon was obviously grumpy, given that he must have been made to wear the red and white Santa Claus hat that was all askew. Rodney McKay was smiling at her then looking hungrily at the spread on the table and then back to her when the person next to him dug a quick elbow into his ribs. Carson Beckett smiled apologetically and shook his head.

She was speechless. The effort that must have gone into all of this. Someone had even managed to line the upper arch of the Stargate with tinsel and a handmade 'Merry Christmas' banner. That could not have been easy.

She knew something was up when she had been cornered in the mess hall by Major Lorne. He had told her that there had been a problem in one of the laboratories and Zelenka needed her help. In the lab, she had been made to sit and translate pages of Ancient text whilst pretending not to notice Lorne and Zelenka looking at each other and nodding every now and again. It was only when she felt the hand on her shoulder and turned to look straight into a pair of twinkling eyes that her suspicions were confirmed. His other hand held the blindfold and he winked. She raised her eyebrow in question but nodded. It seemed a shame for Zelenka and Lorne not to be here considering their key role in his scheme.

Her eyes misted with tears as she looked wondrously around the room. He moved from behind her and stood in front of her, concern visible on his face. Then he saw her joy and smiled. " Hey, Rodney!" he called. "Get the video camera, I think she's speechless!"

Everyone laughed and she laughed with them. She wanted to hug him, to throw her arms around him and never let go. But with an audience anticipating her next action she gazed into the eyes of the man in front of her and did her best to silently convey her gratitude. He gazed back and nodded, understanding what she was trying to say.

He reached forward with his right hand and took her left one again. Then he winked once more and led her to the empty seat at the head of the table. The perfect gentleman, he pulled the chair out and allowed her to sit before gently moving the chair towards the table. He then moved around and sat down to her left.

Finally, she found her voice. "This is amazing!" she breathed. "You didn't have to do all this for me."

Rodney, sitting to her right, spoke first. "It was Sheppard's idea."

She turned to her left. Lt. Colonel John Sheppard shrugged. He was formally dressed (well, as formal as Atlantis could get) in a pair of black trousers and a light blue shirt. His dark hair, as ever, spiked up in several directions - but less than usual so perhaps he had even made an effort with that. He had also shaved and his skin looked smooth enough to touch. His eyes were aglow and the internal argument in which she tried to decide what colour they were reignited - Green? Brown? Both? She had Googled it the last time she was on Earth - the definition that most entries appeared to agree with was hazel. But John's eyes seemed to be in a state of flux, constantly changing colour. It was another feature that added to his overall attractiveness and mystery. Five years they had worked side by side now, he was her closest friend and yet he still managed to surprise her. "John?"

John grinned yet again. "You work so hard everyday. You were even going to work today, weren't you?" She was about to protest but stopped, realising that he was right. Lorne had caught her in the mess hall as she was getting coffee to take to her office. She had allowed herself a lie-in, considering that her celebration of the occasion.

John continued. "I know you wanted to go back to Earth and see your Mom, but, as usual, you put this place first." He shrugged again. "I just thought that, for once, someone should put you first."

As John had been talking, Lorne and Zelenka had entered the Gate Room and taken the two empty seats at the opposite end of the table.

Rodney then spoke up. "Speech! Speech!" Carson, to his right, joined in the chant.

"All right, all right!" she cried over them. Both Rodney and Carson quietened down. She cleared her throat and looked around the table at each person. "I'm not really sure what to say. Thank you all for this. It truly is wonderful and the best Christmas present I have had since I was nine. Everything looks great and well done to whoever decorated the Stargate but never tell me how as I'm sure it would be a health and safety nightmare." There was a quiet ripple of laughter. She picked up her wine glass. "I would also like to congratulate Major Lorne and Doctor Zelenka on their extremely successful task of keeping me occupied in the lab. That was quite a show." Applause broke out and Lorne, followed timidly by Zelenka, got up and bowed. John put his fingers to his lips and wolf whistled. They both sat down and she continued. "Christmas was my favourite time of year. It's strange how you forget things like that when you grow up. Life gets in the way. But when I was a little girl I would be so happy because I would be with my family. Thank you for reminding me what it's like to be with family at Christmas." She raised her glass. Everyone else did the same.

"Hear, hear," said Carson. The group drank collectively from their glasses.

"Great speech, Elizabeth," said Rodney. "Can we eat now?"

Elizabeth Weir laughed. "By all means!"

Dinner was wonderful. In fact, if she didn't know better she would have sworn it had been cooked by her mother and father. But quite apart from the meal was the conversation, the joking and laughter that brought Elizabeth a kind of contentment she was unsure she had ever felt.

As she finished her meal, John leaned over to her, stopping mere inches from her. "So, you like?" he asked, almost seductively.

"I love," she answered, mirroring his tone. "Thank you."

He grabbed her left hand and pulled her put of her chair. Elizabeth apologised for her unceremonious exit through her giggles, allowing her friend to drag her around the table and up the stairs towards the balcony off the Gate Room.

The door slid open to allow them outside. It was a breezy afternoon and the sun was still high in the sky. The waves of the ocean lapped lazily against the city far below their position at the top of the control tower. Elizabeth leaned her right hand on the railing, her left hand still in in John's.

"So," she said as she looked at their joined hands. She exhaled nervously. Why was she nervous? Stupid question. She was well aware of why. Had been for years now. She had tried to stop herself of course. Although there were no strict regulations against it, per se, she was certain the IOA would not approve of a relationship between Atlantis' civilian and military leaders. Also, John was her second-in-command and she had always adhered to her personal rule of never getting involved with anyone working under her.

John Sheppard, however, was different. She had known it the day she laid eyes on the handsome pilot as he sat frozen in the Ancient chair in the Antarctica outpost all those years ago.

_"Who is this?" she demanded to know as she ran into the chair room with Carson Beckett, Rodney McKay and General Jack O'Neill._

_Jack stopped beside the chair and looked down at him. "I said don't touch anything!"_

_His voice shook as he explained. "I-I just sat down."_

_"Major," ordered McKay, "think about where we are in the solar system." Immediately the space above their heads glowed as a holographic display of the solar system appeared._

_"Did I do that?" Major Sheppard asked, puzzled._

His kind face, his sexy gravely voice, the way he held himself, all served to form an immediate attraction. Of course, Elizabeth had not seen it as anymore than that, happy as she was with her partner, Simon Wallace. Anyway, he was so far removed from the kind of man she could be involved with that she immediately dismissed it as a superficial crush.

She brought him all the way to Atlantis. And, although it hadn't been part of the plan, he had become the military commander. As they worked together in the running of the expedition, she had felt the attraction towards him slowly grow. She spent nights in bed listing the reasons she could not fall for him; he was a military man and she had spent her career fighting against the need for the military, he was cocky and arrogant and ready to argue with her over just about anything. She had someone waiting for her. But even as she listed his bad points in her head, her heart immediately countered with good points; he had a strong moral compass and despite being in the military he had been known to disobey orders to satisfy that sense of morality. He was intelligent, so intelligent that he could give some of the scientists on Atlantis a run for their money. He challenged her in so many ways. When he believed in something he would fight and argue for it all the way. He was strong and he was passionate.

It was a conscious decision on Elizabeth's part to ignore the growing feelings. War with the Wraith, the daily running of the expedition and dealing with the various crises that occurred made it easier. So it was a big surprise to her when, two years after they met, she realised it was too late. Doctor Elizabeth Weir had fallen in love with Colonel John Sheppard.

"Elizabeth?"

She looked up to see John watching her quizzically. "Mm?" was all she could respond with.

"You faded out there for a minute," John said. "Where were you?"

Elizabeth smiled self-consciously. "Antarctica, actually."

"Really, why?"

"Oh," she sighed, "I was just thinking how different my life would have been had a certain Major not sat in that chair."

"Different, good or different, bad?" he asked, leaning in as if eager for her reply.

"Well…let's put it this way," Elizabeth said, wishing to prolong the length of time he was this close to her. "It certainly hasn't been dull."

"That's true." They both laughed tentatively. He didn't pull away.

"So, why did you bring me out here?" Elizabeth asked.

"I wanted to give you to your present," he answered quietly. "Close your eyes."

Elizabeth did as she was told. The butterflies started fluttering in her stomach again. She felt her left hand being opened, palm up and something cool being placed in it. Her hand was then closed around the mystery object.

"Open your eyes now," he whispered.

She did and looked down at her fist. She slowly opened it. Her breath caught. There in her hand was a gold chain, thin and delicate. She picked it up carefully. An exquisite princess cut emerald set in a gold pendant hung from the chain. "John, it's beautiful."

"Glad you like it," John said, grinning from ear to ear.

She handed the pendant to him. "Could you help me put it on?" She turned around, lifting her hair from the back of her neck.

John weaved the chain around the front of her neck. Elizabeth could feel his breath in her hair. She closed her eyes at the sensation. She felt him latch the chain on the back of her neck. He then ever-so-gently stroked the area, just below her hair. She shuddered at his touch. She felt his hand move to her shoulder and he slowly turned her to face him. She dropped her hair back down.

"I knew it," he said, his voice just above a whisper.

"What?" Elizabeth asked, keeping her voice low as well.

"It matches your eyes," he said.

Elizabeth blushed and looked down at the floor. "I'm sorry I didn't get you anything."

John took a step towards her and put his fingers under her chin, lifting her head until she met his eyes. She wanted to look away again, the intensity in his eyes almost too much to bear. But she didn't.

"There's just one thing I want from you, 'Lizabeth," he said.

Before she could ask him what that one thing was, John leaned in and placed his lips gently on hers. It was only for a few seconds but in that moment Elizabeth Weir had never felt more alive. She didn't want it to stop. She looked into his eyes and could see the nervousness growing. He wasn't sure she had wanted it.

Elizabeth briefly toyed with the idea of pulling away and feigning upset. She decided, however, to put him out of his misery and put her hands on each cheek and kissed him. John's arms quickly moved around her and pulled her to him, passionately responding.

When they finally stopped, Elizabeth, still in John's arms, laughed softly.

"What?" John asked.

Elizabeth put her arms around John's neck and said simply, "Best Christmas ever."

John pulled his arms down from behind his neck. "Let's get back inside. Rodney planned party games!"

Elizabeth shook her head. "You're kidding!"

"Nuh-uh."

John turned her to face the door, hands on both of her shoulders, lightly pushing her ahead of him.

The door opened and Elizabeth stepped inside. The Gate Room was dark. The confetti was gone, as were the giant snowmen in the Control Room. She looked down to the Stargate. It was bare and there was nothing in front of it. Ronon, Teyla, Rodney, Carson, Lorne and Zelenka were nowhere to be seen. It was cold and silent.

"John?" She turned to him but he wasn't there. "John!" she called out. Her voice echoed around the Gate Room. She called out the name again but this time her voice sounded different. It was higher, softer, wrong. It was not her voice.

Elizabeth ran down the stairs to the Stargate. She looked down the corridors that led out of the Gate Room. They were dark. She ran up the stairs to the Control Room. She looked at the various consoles and bashed a couple of the buttons on the Dial Home Device. It was all dead.

She sprinted across the bridge into her office. Her laptop was on her desk and there was a light coming from the screen which faced away from her. Elizabeth rounded the desk and leaned towards the screen. But all she could see was a face looking back at her. She was a young woman in her late twenties or early thirties. She had a kind face and a pale complexion. Her eyes were brown and her brown hair was longer than her own - and very straight.

As she stared, Elizabeth realised that the face seemed to be matching her movements. Slowly, she put her left hand up and touched her eyebrow, watching in horror as the same thing happened on the laptop screen. She moved her hand to the top of her head. The movement was mirrored.

Mirrored. Her actions were not being copied but seemed to be reflected, as if this was her face. She stared at the face, not knowing what to do. If only John was here. He would know what to do, what to say. How she missed him.

Before her very eyes, something started happening to the face in the reflection. It was turning paler and she could see tiny icicles building around the eyes and nose. The lips turned blue. As it happened, Elizabeth could feel her own body growing colder and colder. She moved her hand from her hair feeling how difficult the action was. Numbness was setting in and she was so, so cold but she couldn't shiver. She closed her eyes, a vision of John Sheppard in her mind.

Everything went black. Then she could see small pin pricks of light against a pitch black blanket sky. Something floated nearby her line of vision. It took her a moment to register it was the body of a man.

It all came flooding back. Her near death, the reactivation of the inert nanites in her system, her capture by the Replicators. The torture, the pain. The loss of her body as she attempted to ascend. Her return to Atlantis and the creation of a new body for her to inhabit. The look in John's eyes when he told her, "_You may still think you're Elizabeth, but you're not."_

She had stepped through the Stargate, knowing it was a trap. And she had floated in space ever since.

Christmas. It was Elizabeth Weir's favourite day of the year. And it was gone. The Christmases of the past, the Christmases of the future. All of it gone. He was gone.

A Replicator, one that once knew itself to be Doctor Elizabeth Weir, screamed silently.


	2. Chapter 2

**Chapter ****2**

Lieutenant Colonel John Sheppard stood on one of the many balconies of the great city of Atlantis. Across from the city was the stunning Golden Gate Bridge, crowned by low clouds.

He stood with his friends, Doctor Rodney McKay, Doctor Jennifer Keller, Teyla Emmagan, Ronon Dex, Amelia Banks, Doctor Carson Beckett and, yes, even Richard Woolsey as they chattered away, enjoying the breathtaking view. He didn't hear what anyone was saying and didn't care to either. He heard them laugh and laughed as well, although he had no idea what it was about. But he didn't want them to see he had something else on his mind.

Atlantis had been her dream and she had been the one to lead them to it in the faraway Pegasus Galaxy. For three years she had kept the city safe, giving her own life in order to protect it - not once, but twice.

Now Atlantis was on Earth, its original home. And Doctor Elizabeth Weir should have been the one to bring it here. But she wasn't. She was alone, floating in space, trapped in the frozen body of a Replicator.

At the time of the entity's arrival, John had been very wary of accepting its claim to be Elizabeth. When the entity had taken it upon itself to create a body to inhabit he had been more convinced that this entity was either an impostor or that Elizabeth had been so infected by the scourge of the Asurans that she was no longer recognisable as the woman he…

Sheppard had never been happy with the plan. Not once she had told them that she couldn't guarantee the safety of Atlantis from the other Replicators. That had sounded like his Elizabeth, the Elizabeth Weir he trusted with his life. As she had walked towards the event horizon he had stepped forward, wanting more than anything to stop her. She turned back and their eyes locked, just as they had done so many times before. And she nodded to him. She understood. She knew it was a ruse but wanted him to let her go.

In his life John Sheppard had done a lot of stupid things. He was known for it in fact. However, he only had two regrets in his life. Both related to her. He would never forgive himself for leaving her on Asuras. Sure, she ordered him to but since when had he been the poster boy for following orders? Then, not only did he leave her, he never went back for her. He had politely asked the IOA to authorise a rescue mission and then made another request to the new leader of Atlantis when she arrived. He accepted their negative responses and continued with his life. Why? Why had he even bothered asking? He had been in charge during the weeks it took the IOA to select Samantha Carter as the new expedition leader. Why hadn't he just gone back for her then? He wasn't sure he would ever know the answer to that.

His second regret was allowing the Replicator he knew to contain the consciousness of Elizabeth Weir to walk through that 'Gate. He should have made the other Replicators go first and shut the wormhole down before she could go. He should have run forward and pulled her away.

He should have told her. He should have told her the truth. Elizabeth Weir had given John Sheppard something that no one else had ever given him: a chance. A chance to prove himself. He would always be grateful to her for that. Before he'd met her his life was a mess. He was nothing more than a gloried chauffeur, ferrying important people around over the wastes of Antarctica. But she had discovered his ATA gene and immediately asked him to join the expedition. She wasn't even put off by his previous record. And when Colonel Sumner had died - ultimately by Sheppard's own bullet - she had trusted him to be the military commander of Atlantis. He knew that when the SGC brass had tried to take that command away from him, she fought to keep him, even demanding he be promoted - she never told him about this, General Landry had been the one to fill him in after she was lost. The life he was living right now was down to her and John had never told her how thankful he was.

He was just so bad when it came to talking about his feelings. It was not a skill that had been instilled in him from a young age. He barely even remembered telling his mother he loved her and he had only been eight when she died. He certainly didn't remember ever saying the 'L' word to his father and Dad probably would have been horrified if he did. His ex-wife cited his inability to talk as one of the reasons for filing for divorce.

He remembered once telling Teyla that he would do anything for his friends, even die for them. He had even mentioned Elizabeth by name. But he had never said anything to her. How he needed to protect her, how he would go to Hell and back for her. How much he valued their friendship. How much he loved her.

Elizabeth was the only person John had ever dreamt of having a future with. Sometimes he would imagine her in the white wedding dress he had seen his mother wearing in photographs. Other times he saw them living daily life in a little house in the countryside. It was strange. His mind could conjure up what some would have thought to be a mundane existence but for him it felt like a great adventure to be fully savoured and enjoyed.

So, not two regrets. Three regrets. And all of them were involved her.

John felt a hand on his own and looked over to see Teyla looking at him. She was concerned. No wonder, he realised, as he saw that she was here alone with him. He hadn't even noticed the others leave.

_Well, how to get out of this one?_

John Sheppard could see determination in her eyes and knew he didn't stand a chance. So, he smiled - as much as he could anyway - and waited for her to start the conversation.

"Are you all right, John?" she asked.

John shrugged nonchalantly. "Sure." He paused. "Just been a big day, you know."

Teyla nodded and, for a moment, John thought he was going to get away with it.

Wrong. "John," she started, "how long have we known each other?"

"Five years," John answered straightaway.

"A long time," said Teyla. "I understand you are a proud man but you have been different for some time now. Distant. It does not do to keep your feelings within."

John immediately felt irritated. It wasn't her fault, it was his. But having known each other for five years she knew that when it came to John Sheppard's inner turmoil it was best to leave well enough alone. "I'm fine, Teyla," he said sharply.

"You miss her."

John froze. How could she know? They had never really talked about Elizabeth except in passing for two years now. Even after she had left five months ago in F.R.A.N's body they had continued their daily routines with very little discussion. "Who?" He wasn't going to give in to her. If he admitted it then…

"Doctor Weir." Teyla's soft voice exuded patience.

Sheppard looked down at the railing, then out to the bridge. Part of him wanted to be honest. Teyla was kind and would never judge him. It just wasn't who he was. He didn't burden his friends with his issues. That was not what friends were for. Hell, if he told a friend all the crap that had gone through his head since he had joined the Air Force he was pretty sure that said friend would have gone into a catatonic state. He never considered it a good idea to share his pain.

What if he did tell her? Would the cliché about a problem shared is a problem halved be true? Would he release his burden? He smirked. Release his burden. Next thing he knew, he would be ready for ascension.

He decided to try and deflect her one more time, sure that she would finally get the message. "I don't know what you mean."

Teyla sighed. "John, I said that you have been different. I am not the only one who has noticed this change in you. You have been this way ever since Elizabeth was left on Asuras. I had hoped that with time it would pass but it has not. She paused. John said nothing. "Today, we are on your homeworld after saving it from a Wraith attack. We are all here... and yet you do not seem happy."

He said it without thinking. "But we're not all here, are we?"

Teyla smiled sadly. "No, we are not."

John looked into her eyes again and saw only kindness and sympathy. For three years he had been quiet. He had flirted around the issue but never taken the chance.

"You're right, I do miss her." He stopped, waiting for a response, almost expecting laughter. There was none. He took a deep breath and tried to continue. "I… you know me, Teyla… um, I'm not good at this feelings stuff…" he trailed off.

"Teyla's hand touched his arm gently. "I know."

"She should be here with us." John pushed himself to make himself clear. "With me."

Teyla looked startled. "John, I -"

"I'm sorry, " he blurted out. "I shouldn't be…" he stopped, pulled his arm away from her touch and looked away.

Teyla moved around to face him. Were there tears in her eyes? "You loved her." It wasn't a question.

Sheppard couldn't speak. It was the first time he had heard words to that effect spoken aloud. He closed his eyes, unable to take the pity he could see forming. He nodded once.

"I knew that you were close to each other and… we sometimes talked about whether there was something going on," Teyla said softly, "but I had no idea you felt that way."

"Well, I did," John said, his own voice timid. He suddenly felt a rage within him and turned and slammed the railing of the balcony with his hands. Teyla jumped slightly. He spun around to face her but looked up to the sky, hands on his hips. "Who am I kidding? I still love her." He could hear the desperation in his voice.

"I am sorry," was Teyla's response.

John nearly smiled. Somehow it did feel better telling someone. And Teyla was so understanding. Perhaps he had been missing something all these years. Maybe it really was good to talk. But now what? There were no solutions to his problems, there was no way out.

Teyla tried to find one anyway. "Did you not tell her?" He shook his head. "I am unsure as to how deeply Elizabeth's feelings towards you were but I do know that she considered you her closest friend. She would not wish this life for you."

"And what life would that be?" he retorted.

"A life in which you feel very little but pain and suffering. You do not deserve it."

"But I do!" John nearly shouted. "Don't you get it, Teyla? I betrayed her - twice. I was supposed to protect her and I screwed up. And now she's gone. You know, it would be better if she was dead. Maybe then I could kid myself that she's in a better place. But she's not. And that's all down to me." John bent forward and rested his forehead on the railing, the cold metal nearly jolting him back up.

Teyla's hand came to rest on his shoulder. He thought about shrugging it off but she spoke. "Elizabeth would disagree with you and I am certain that her opinion matters to you, even now." She paused before continuing. "If you choose to continue living as though you are a shadow then you dishonour her and the high regard in which she held you. You must find a way to be at peace with yourself."

Teyla's words faded as John stood up straight. What the hell was he doing? This was ridiculous. All he sounded like right now was a pathetic girly loser. And John Sheppard was not girly. Damn it, why did he ever think this was a good idea? He had never told Elizabeth for fear of jeopardising their careers on Atlantis (and also for fear that in all likelihood she would not feel the same) and once she was gone it was easier to put those feelings in a box and pretend they didn't exist. But now, telling Teyla meant that it was all too real. And actually, he didn't feel better, he felt worse. God, he _was_ pathetic. So utterly pathetic. He needed to not be here.

"I gotta go," was all he could muster as he all but ran for the door, leaving Teyla behind without looking back.

He speed walked his way to his quarters, not paying attention to the route he was taking - he knew the city so well he didn't really have to - or the people he passed.

It was only as he arrived at the doors that he realised what he had done. He passed his hand over the sensor to the left of the doors and stepped inside as they opened.

The room was dark. He passed his hand over the sensor on the left wall and a light came on. Unsurprisingly, the room was devoid of personal items. All that was left was a single bed, a desk and a chair. The view of the city by her bed was gorgeous. No one had used this room after she went. When Carter arrived to replace Elizabeth, there was still hope that she would return so her room had been left as it was. After that it was always considered to be her quarters and no one had even considered assigning them to someone else.

When the clone of Weir had told him his Elizabeth had been killed by the Asurans, John had come here and put all of her personal possessions into a couple of boxes - well, most of them. It had been so painful that he didn't return to the room until she left the last time. The night after she had gone through the Stargate he had come here and stood in the middle of the space. He whispered the words, "I'm sorry, Elizabeth," and left again.

Why was he here now? He did not know. One thing he did know was how awfully drained he felt. It had been a crazy day, after all. He walked slowly to the bed. There was no bedding, just a pillow and a mattress on the frame. He dropped down onto it and lay flat on his back, staring up to the ceiling. Within minutes, John Sheppard was sleeping.


	3. Chapter 3

A/N: Hi. Hope everyone had a good Christmas and New Year. Thanks to everyone who has left a review and decided to follow the story. No pressure now, eh! Anyway, here is Chapter 3 - enjoy!

**Chapter 3**

The consciousness of Doctor Elizabeth Weir wished she was able to cry. As she surveyed the scene before her, she considered the possibility that it was not real. She could not even say if F.R.A.N's eyes were open but she did not think so. She remembered slowly turning and seeing the other Replicators as they came through the Spacegate… and then yes, her eyes drifted closed. In all likelihood, they were still closed, given the effect that floating in the freezing vacuum of deep space had on an artificial body.

So, was this another illusion of her incredibly active…imagination? Did Replicators imagine? Or did they construct scenarios based on available pertinent data?

The usual questions came to her. Who was she? What was she? Should she still even think of herself in terms of gender? In terms of a person? In the terms of Elizabeth Weir? However, despite everything that had happened to her in the last two years, the consciousness still felt like Elizabeth Weir. More so, since she had been here. She had all of Elizabeth Weir's memories. All of her feelings. She felt as though she thought in the same way as Elizabeth Weir.

During her time in this body, the consciousness had constructed so many scenarios. In one Elizabeth Weir never became part of the Stargate Programme. She worked in New York at the United Nations until she was sent to Afghanistan to negotiate the military withdrawal and handover of power. Here, she met an Air Force colonel named John Sheppard…

Elizabeth Weir was a student at Harvard, studying Law. One evening she was walking through the main plaza when she was grabbed from behind. She screamed and she and her would-be attacker were knocked to the ground. There was a scuffle between what looked to be two men nearby as Elizabeth tried to collect herself. One of the men got up and ran away. The other then got up and put his hand down to her. She took it and he gently pulled her up. Even in the dark she could see the dazzling green/brown eyes…

Elizabeth Weir was walking – no, gliding – down the aisle of a church, her father to her left. As she reached the altar, a man in a dress blue Air Force uniform turned to look at her and grinned. "You're beautiful," he whispered…

Elizabeth Weir was lying on a beach. The sea was gently lapping nearby and she could hear sniggering. She decided to pretend she couldn't hear it and kept her eyes closed, making soft snoring sounds. Suddenly, she was hit by what felt like gallons of water. She sat up sharply and grabbed the first body she could. A boy, no more than six-years-old with green eyes and crazy black hair laughed hard as she tickled him. She looked up from the boy to see him further away, doubled over in hysterics. "John Sheppard, I'm gonna get you for this…"

The problem was that no matter which scenario the consciousness created they always ended the same way. With the realisation of the horrors she had been subjected to and where she had ended up. Why couldn't she keep the illusion going? Why did she always ruin whatever wonderful thing was happening? Why was she always surprised when she remembered the truth?

Not for the first time, the consciousness wished she was dead. That she had died when the Control Tower had been grazed by the Asuran laser beam. Everything that had happened to her since Jennifer Keller and McKay had reactivated her nanites had been harrowing. She had been captured, changed, probed and violated in the most horrific ways. She had been made to believe that Atlantis had been destroyed, that her friends had been killed. Oberoth and the other Asurans had created such elaborate and detailed scenarios that there had been many times she had believed them and she was nearly driven insane. If she had died then she would not have suffered such cruelty.

The consciousness remembered the hurt she felt when John Sheppard had told her she wasn't Elizabeth. Now, she kind of understood it. Elizabeth Weir's consciousness still felt like the woman she had come from but she was also different. The experiences she had been through had changed her. How could they not? In the past she would never have even considered lying to John. But she did. She had brought a group of disembodied _Replicators_, knowing the danger they posed Atlantis and the Expedition but she felt it was the right thing to do and that the Replicators would be happy for her to take the lead. How wrong she had been.

However, when she stepped through the Stargate to end up here she realised she had a choice. The other Replicators were waiting for her signal to tell them she had safely arrived at their destination. But if she warned her companions they would have brought Atlantis to its knees and she could not allow that. The right thing to do, the thing that Elizabeth Weir would have done, was to send the message that it was safe. And it was as though in that moment the consciousness truly remembered what it was to be Doctor Elizabeth Weir, even if her soul had been destroyed and this...shadow was all that was left. Atlantis was her life and she gave everything to protect it.

Even in her current (and unchanging) predicament, the consciousness had no doubt that she had done the right thing. Atlantis and its people lived on, saving the Pegasus Galaxy, one crisis at a time.

The desire to be there on Atlantis with Elizabeth Weir's people was so incredibly strong. To be in charge again in the everyday running of the city, to be sitting through meetings with the various teams – even the interminable botany briefings – to be arguing with Rodney, drinking coffee until the early hours, conversing and subtly flirting with John.

Maybe that was it. Maybe the reason the scenarios all fell apart was because the consciousness couldn't help but focus on the happy ending. The real Elizabeth Weir was not naïve. She understood the difference between real life and fantasy and would never accept the latter. But what if the scenario was not a fantasy but just the life she remembered before?

Well, it was worth a try. It had to be better than just floating and contemplating the nature of her existence.

* * *

Elizabeth awoke with a start. Where was she? She rubbed her eyes and sat up cautiously. She was in bed. Her bed. In her quarters on Atlantis.

She was so tired but looked at the clock on her bedside table: 06:30 hours - time to get up. She pushed the blankets aside and got out of bed.

She walked to the adjoining bathroom, the light activating automatically as she entered. As she looked into the mirror she jumped. She didn't know why. She studied her reflection to see that all was present and correct. Brown hair that went just past her shoulders, the kinks in each strand proof of the fact that no matter how long it got the natural curls would not go away completely. Ivory skin with light brown freckles that could only be seen on her face if one looked closely enough. Tired green eyes. She smiled and breathed a sigh of relief. What she was expecting when she looked in the mirror she did not know but she was surprised to see her own reflection.

She was looking quite thin in the white tank top and pink tartan pyjama bottoms. Probably due to lack of sleep and missed meals. Strangely, she did not remember going to bed last night. In fact, she couldn't recall the last time she had a decent night's sleep. She felt so utterly drained right now, she could fall asleep standing as she was.

She briefly thought about going to the Infirmary. Jennifer Keller would probably be happy to give her something to help her sleep tonight. But, truth be told, Elizabeth never felt truly comfortable in her care. She was not sure why but she didn't feel like she could… trust her. That sounded terrible! Of course she trusted Jennifer; otherwise she would not have put her in charge of the health of everyone on the base. But, there was the difference. She trusted her to look after everyone else but not herself. It didn't really make any sense but whenever she saw Keller she felt immediately on edge. She couldn't even think of a time she had gone to see her for her own medical care since Keller took the role of Chief Medical Officer. And Elizabeth knew that if Carson was still around she would be going to see him before breakfast.

* * *

Elizabeth left the mess hall with a scalding cup of coffee in one hand and a paper bag containing a cream cheese bagel in the other. As she approached the transporter she felt the presence of someone behind her.

"Hello, John," she said, without turning around. She went to open the transporter doors with the hand holding the bag but his hand got there first, brushing hers as it swished over the sensor. She quickly pulled back.

"Let me get that," he said cheerfully. The transporter doors opened and John stepped aside for Elizabeth to enter the booth first. He followed her in. "And how are you on this fine morning?"

"Not nearly as chipper as you," Elizabeth said, her eyebrow involuntarily rising at his inexplicably good mood.

"Yeah," John replied. "You don't look so great." He pressed the marker on the city map on the back wall that indicated the transporter nearest the Control Room. The doors closed, a light flashed and the doors reopened.

Elizabeth exited first, making sure John did not see the hurt before she had a chance to cover it up. "Thanks for that."

John hurried after her and took up the space to her left. "No… I meant…" he fumbled, "you don't look as great as you normally do."

Elizabeth slowed her pace and smiled a little. "Nice save," she teased. "You could try to be more tactful next time."

"Sorry," said John sheepishly.

They entered the Gate Room and walked up the stairs to the Control Room consoles. Chuck, the technician, and Rodney McKay were arguing over the DHD console.

"Good morning, gentlemen," Elizabeth said over the bickering as she and Sheppard came to a stop in front of the DHD.

Both stopped arguing and looked over. "Good morning, Doctor Weir," answered Chuck politely, clearly embarrassed at being caught behaving so unprofessionally.

"You look terrible," said Rodney at the same time.

The eyebrow went up again, this time deliberately. "Excuse me?"

"McKay," John said the warning clear in his voice.

"I just… I meant…" Rodney sighed sadly. "Sometimes I shouldn't speak."

"You got that right," said Sheppard. "And you tell me I need to be more tactful," he directed to Elizabeth.

"You look tired," said Rodney after a deep breath.

"What's the problem here?" asked Elizabeth, making the difficult decision to let McKay off the hook.

Rodney looked relieved but his expression quickly turned to one of irritation – what John called his "default" face. "Well, Mr Genius here has broken the Stargate."

"I have not!" said Chuck, defensively. "I told you, I was running the morning diagnostics as normal and… I don't know what happened… but sparks started flying out of the DHD. The Stargate itself is fine."

"Oh, I'm sorry," said McKay, sarcastically. "Are you the foremost expert on Stargate technology on this base?" When Chuck wearily closed his eyes, McKay answered his own question. "Oh, no, that would be me!"

"So, what's wrong with the Stargate?" asked Sheppard.

"Oh, come on, you could at least give me a chance to figure it out," whined McKay.

"Well, I'll be in my office when you're ready," Elizabeth said with as much patience she could muster. She walked away, turning back just in time to see Sheppard lean up over the DHD and smack the back of Rodney's head. She sighed and shook her head. Sometimes this job was running a city, sometimes it was trying to save the galaxy. But a lot of the time it felt like babysitting a bunch of petulant children.

* * *

He had been watching the bodies for some time now. All of them had been here frozen when he arrived. He looked at most of them and felt nothing at all. They were not human, they were Replicators – Asurans they called themselves. The final one was a female. She wore and off-white suit of trousers and knee-length top. She had long brown hair.

He had never met this Replicator before but he sensed something in her, something he did not sense in the others. And he recognised it.

* * *

Elizabeth sat down behind her desk and took a sip of coffee, then a bite of her bagel before booting up her laptop. Going through her new e-mails, she decided to leave McKay's until after the morning briefing which was in half an hour. There were seven and she knew they would each consist of epic tales and stories, followed by gripes with members of his staff and ending with a request for her to authorise something. These requests could range from the perfectly reasonable to the downright crazy.

John entered the office and sat himself on the front left corner of her desk, just as he always did.

"Any update from Rodney?" Elizabeth asked him.

"At the moment, all he can say is that the DHD is out of action. The Gate seems to be okay." He paused. "I think this may put the brakes on our mission to P3X-912."

"No kidding," said Elizabeth.

There was silence. Elizabeth looked up from the computer screen to see John scrutinising her. She waited until he seemed to realise she had noticed and he averted his eyes to just over her shoulder. She was a little disappointed.

"Are you all right?" he asked, his tone laced with worry.

"I'm fine," Elizabeth lied.

"'Lizabeth," John said firmly. "Not to defend Rodney and his monumental knack of saying the worst thing but if even he's noticing something then it must be pretty obvious."

Elizabeth sighed. What could she say? John's logic was flawless.

"I'm tired," she finally admitted. It was some of the truth anyway.

John didn't say anything. His eyes gazed intently into hers.

It did the trick. "Have you…?" she chuckled. "No, it's stupid."

"Go on," John coaxed.

She looked down at her hands as she clasped them together nervously and smiled. "Have you… ever woken up feeling like something was… off?"

"Off?"

"Like something just wasn't right," she clarified. "But you can't figure out what it is?"

* * *

The entity moved towards the female Replicator body and reached out tentatively. The "mind" within was not conscious but he could feel that the subconscious was… active.

It was her. He was certain of it. It had been ten thousand years since he had met her but the little time they had spent together had had a profound impact upon him.

Curiosity got the better of him. The others would probably be displeased by the course of action he was about to take but he had to do it. She needed help and he could provide it.

Carefully, he reached further, attempting to connect with the subconscious.

* * *

John's head bobbed slowly from side to side, as if weighing up what Elizabeth had said. Probably considering whether she might be going crazy.

"That's a no then," Elizabeth said.

"Well, I guess everyone feels it at some point," said John reassuringly. "I don't think it's ever caused me to lose sleep though. How long have you felt this way?"

"I don't know, a while, I think." Elizabeth couldn't clearly remember much beyond waking up this morning.

"Maybe –"

An alarm sounded from the Control Room. John and Elizabeth jumped from their seated positions and looked through the glass wall down to the Stargate. One of the chevrons was alight.

"Incoming wormhole!" Chuck shouted out.

They both ran out of the office and across the bridge to the Control Room. Rodney and Chuck were studying their computers.

"We're not expecting any teams back, are we?" Elizabeth asked Chuck, although she knew the answer.

"No, Ma'am," confirmed Chuck. The chevrons continued to light up.

"Lorne's team are due back tomorrow," said Sheppard. "Maybe they ran into trouble."

The seventh chevron lit and the Stargate activated. The great pool shot out and back to form the shimmering event horizon. A team of armed soldiers spread themselves around the steps up to the Stargate.

"Raise the shield," said Elizabeth, even as the translucent bubble formed in front of the Gate. "IDC?"

Chuck shook his head.

John left the Control Room and started walking down the steps. Elizabeth followed.

The shield started to flicker. John indicated to one of the marines on the floor who passed him a nine millimetre handgun. John flicked off the safety and moved across to stand in front of Elizabeth. "Rodney!" he called as the shield continued to flicker.

"I don't know what's happening!" McKay yelled back. "There's no reason for the shield to be de-stabilising."

The shield dropped. John aimed his gun towards the event horizon, as did the other soldiers. Elizabeth held her breath.

A being of what appeared to be pure light glided out of the pool. It had tentacles and glowed magnificently.

Elizabeth exhaled. "Oh, my God. An Ascended being."

The being's light dimmed and it transformed before their eyes. A tall Caucasian man with dark blond hair who looked to be in his late thirties stood in its place. He wore an off-white outfit of trousers and shirt, eerily similar to those worn by the Asurans.

The man looked at the people around him. He then saw Elizabeth behind John and a smile spread across his face.

"Hello, Doctor Weir," he said in happy voice with a charming English accent.

Everyone seemed to turn to Elizabeth. Even John had half turned his head to look at her but still had one eye and his firearm trained on the stranger.

"I'm sorry," Elizabeth said slowly, keeping her tone neutral. "Do I know you?"

The man smirked. "In another life," he replied. "My name is Janus and I have a proposition for you."


	4. Chapter 4

**A/N:**Hi everyone. Thanks for coing back. sorry, this is up a little later than planned. Had slight technical difficulties which had to be sorted out - mostly by hoping. It worked! Anyway, quick answer to PureSummerMagic's question. Chapter one - Christmas on Atlantis never actullay happened, it is imagined.

**Disclaimer:** I haven't done one since the first chapter as I kind of thought that was enough. But I'm going to do one anyway. I don't own anything or anyone related to Stargate. If I did you can bet things would have been different.

**Chapter 4**

Light. Evil, unwanted morning light. Lieutenant Colonel John Sheppard opened one eye and confirmed it was in fact daytime. He groaned and closed the eye again.

His head felt like it was going to explode. To wake up feeling like he had the worse hangover without getting incredibly drunk the night before – it really wasn't fair. Someone hated him, he was sure of that.

But… he was alive. It could have very easily been the opposite yesterday. However, that didn't make him feel any better. For John, the word 'alive' had many different interpretations. In his case he was alive insofar as he was breathing. But nothing more.

Teyla was right. Yesterday he saved the world. And he was only breathing. He may have felt relief when they escaped through the Stargate after ensuring the Wraith Hive's destruction, but honestly, he felt more content when he had been sitting in his F302 on the Hive waiting to sacrifice himself.

He should have felt… happy? Maybe. Glad to be alive? Definitely. He wasn't. He felt… nothing. Nothing but…

_"You loved her."_

Sheppard's eyes flew open and he bolted upright. The memories of his conversation with Teyla replayed in his mind. He put his face in his hands and shook his head. "Good one, John," he mumbled, ashamed. "What were you thinking?"

Taking his hands away from his face, John allowed his eyes to focus on his surroundings. _Damn it,_ he thought. He was in her room, on her bed.

He got off the bed and walked to the window. The spires of the city shone majestically in the light of the morning San Francisco sun. He contemplated the question of what would become of Atlantis now. It couldn't stay here. John couldn't see the feasibility of putting Atlantis on one of Earth's oceans without the general public finding out either. Nevertheless, Earth was Atlantis' original home planet. He could imagine the IOA wanting to keep it here or at least nearby. That thought did not sit well. Atlantis belonged in the Pegasus Galaxy, defending the people who lived there in fear of the Wraith. That was what his instinct was telling him and he was in no doubt that Elizabeth would have felt the same way.

His mind returned to the subject it had been trying to avoid. What had possessed him to profess his feelings to Teyla? Didn't she have enough on her mind already with her partner and son in another galaxy? Now she was probably worried about him and Sheppard could not abide that. How could he do this to her, how could he be so selfish? And to what end? All their "chat" had succeeded in doing was making him retreat to her quarters.

He looked around the room. Although none of her things were present it still felt like she was here in the room with him. His heart lurched in his chest and his eyes involuntarily began to well up. He clamped them shut to stop the tears escaping but he could only see her. Here, in his mind, she stood on the balcony – their balcony – and watched the ocean. It had been her favourite place. Consequently, it had become his favourite place too. They had spent so much time there, talking, laughing, and arguing. Sometimes they stood side-by-side in comfortable silence. Sheppard had never experienced the kind of serenity he felt when he stood with her out there, gazing at the vista before them, without the need to exchange words.

"Colonel Sheppard."

Sheppard's eyes opened and he put his finger to his left ear to activate the earpiece. It was Richard Woolsey. Back to business.

"Sheppard here."

"I've just received word," said Woolsey. "A delegation will be arriving on Atlantis in two hours."

"Wow, guests already," said Sheppard, assuming his role as Atlantis's cool military commander. "Is the President coming? 'Cos if he is we'll need to break out the bunting."

There was a pause and John could almost see the look of exasperation that was likely to be on the civilian leader's face. "No, Colonel, but members of the IOA, Homeworld Security and Stargate Command are so I would appreciate it if you were present when they arrived."

John sighed. "Yes, Sir."

"Oh, and Colonel."

"Yes."

"Please make sure you are appropriately attired."

"Yes, Sir." Sheppard cut the connection and groaned. _Appropriately attired_ – he knew what that meant. God, he hated the dress blue uniform. Sure, it looked good but it was a bitch to put on and he was never comfortable with the formality of it.

He had two hours so he decided the best thing to do was to head to his quarters to prepare. He walked to the doorway, pausing to look back at the room. "Bye, Elizabeth," he whispered, then used the sensor panel to open the doors.

As he walked to his quarters, he contemplated his next move. He needed to talk to Teyla. But what would he say? Should he apologise for burdening her? Should he tell her to forget it? Should he tell her he was joking? That would go down well. _"Hey, Teyla, that stuff I told you about being in love with a woman I can never have? Just kidding!"_

Maybe evasion was a better idea. Obviously he couldn't literally avoid her as she was his friend and a member of his team. But he could certainly avoid talking about it. If he acted as though it had never happened, she would get the message. He was sure she wouldn't be happy about it but she wouldn't push it – well, not again, anyway.

_Sounds like a plan_, John thought as he arrived at his quarters. He opened the doors and entered. He had a delegation to get ready for.

* * *

John Sheppard looked in the mirror and again adjusted his tie. It didn't look quite right.

Finally, he pulled the tie off and started again. As he did, his thoughts wandered to the last time he had worn this uniform.

_He stood nervously on the porch as he waited for an answer._

_The white door opened. A woman greeted John with a polite hello and a look of confusion. She was in her sixties with ivory skin and her dark hair with silver lining was naturally curly. But what struck him the most were the identical green eyes. It took him a moment to remember that he had to say something back._

_He cleared his throat. "Mrs Weir," he stated shakily, "my name is John Sheppard. I worked with your daughter."_

John shook himself out of the memory. He finished with the tie, buttoned up the jacket, grabbed his hat and stalked out of the room.

As he left the transporter booth he was met by Teyla, Ronon, McKay and Major Lorne. Lorne was also in his dress blues. Rodney wore a grey suit with a blue shirt and tie. Teyla wore a long brown skirt and a faded pink top with flared sleeves. Ronon was in his usual brown leather outfit but with the long brown coat on top – his idea of dressing appropriately.

"So, are we all ready?" John asked jovially. He didn't look directly at Teyla.

Each one of them nodded. John took the lead as they walked the rest of the way to the Gate Room.

He stopped when he saw the podium in front of the Stargate. What was this all about? He looked around the room, up to the Control Room and Weir's – Woolsey's – office. People were starting to fill the rooms, all were dressed smartly. He then noticed Richard Woolsey and Major General Jack O'Neill descend the steps from the Control Room.

As if in telepathic contact with one another, both Lorne and Sheppard stood stock straight and saluted the head of Homeworld Security. O'Neill reciprocated, and then smiled. "At ease, gentlemen."

Sheppard relaxed his posture and nodded his head towards the podium. "May I ask what's going on here, Sir?"

O'Neill smirked. "You'll see."

Sheppard looked to Woolsey who looked far more comfortable in a black suit, white shirt and black tie. When he had taken charge of Atlantis six months ago Sheppard had had severe doubts about his strength of character and his ability to do the job. But, Woolsey had proven himself and, in the process, earned John's respect. Woolsey only nodded, then walked to the podium.

Rodney groaned. "Please don't tell me he's written a speech."

"The Wraith should have let me stay dead," Ronon muttered.

Woolsey tapped on the microphone to see if it was working. It was. Everyone in the area quietened down and gave him their attention. "Good morning," he began. "It has certainly been a trying few days for us all. But, thanks to the efforts of each and every one of you here we were able to avert a terrible event befalling Earth and the Milky Way." He paused. "I can honestly say that I have never been more proud of anyone than I am of all of you." He smiled. "Now, I shall hand over to General O'Neill." As he stepped down, everyone applauded.

The team turned to O'Neill, mouths agape. "Yeah, I may have told him to keep it short," he said just loud enough for them to hear. "You can thank me later." He went to the podium and the applause died down.

"Well," O'Neil started. "I'm not one for epic speeches so we're gonna get right to it. For their unwavering courage and action in the face of a dangerous enemy, it is my honour to promote Major Evan Lorne to the rank of Lieutenant Colonel…" Applause and cheers erupted in the Gate and Control rooms. Lorne was smiling freely.

"And…" O'Neill said loudly and the noise immediately died down. "And Lieutenant Colonel John Sheppard to the rank of Colonel."

John looked to his team who were beaming at him. "Go on," said Rodney.

Sheppard and Lorne made their way up the steps as the clapping began again.

The entire ceremony was a blur. John barely heard the words spoken about Lorne or himself. All he felt was regret that she was not here to see this. At one moment, he thought he saw her standing on the balcony outside her office, overlooking the Gate Room. She was in her standard grey trousers and red T-shirt with her arms folded across her chest. She smiled at him. He blinked and she was gone.

* * *

The party was in full swing. John had asked Jack about the wisdom of having a promotion ceremony and party before there had even been a debrief. O'Neill had put a hand on his shoulder and said solemnly, "Colonel, I have a rule as head of Homeworld Security: party first, debrief later."

The entire expedition seemed to be here, as well as some notable additions – Colonels Samantha Carter and Cameron Mitchell, Daniel Jackson, Teal'c and Vala Mal Doran, along with General Landry, all from Stargate Command. Rodney was making awkward conversation with Carter and Jackson while Teal'c was conversing with Ronon – what those two were talking about Sheppard couldn't guess, but at least they weren't knocking seven bells out of each other this time. Landry was talking with Carson Beckett and Jennifer Keller.

John had made the rounds, mingled with people and made polite conversation. However, he spent most of his time standing on the balcony outside the Gate Room. He rarely came out here now, the reminders of Elizabeth too painful. Today though, all he seemed able to think about was her, to the point where he imagined her presence at the ceremony.

It occurred to him that this was his second promotion since he had met her. He had never expected to be made a Lieutenant Colonel, let alone a full bird Colonel.

God, he really did miss her. It had taken a while for them to learn to work with each other – the number of times in the early days John had disobeyed her orders or disagreed with her methods led to some pretty heated discussions. At the time, they were cut off from Earth and he had only Elizabeth and himself to answer to. So he did what felt right to him. It was only as time passed that he realised that she also had the Expedition's best interests at heart and that if he discussed things with her they may be able to come up with mutually agreeable solutions. Once that had been established a form of telepathy evolved, each of them seeming to know what the other was thinking by the look in their eyes.

Still, when contact with Earth had been established, Sheppard had expected to either be replaced as military commander or for Elizabeth to be so sick of him she would push him through the Stargate herself. But she didn't. She got him promoted to Lieutenant Colonel instead – and made him feel he was worthy of it.

This promotion, though, this celebration – he did not deserve it. He had done the one thing that he never wanted to do –had never done before. His rule, his code: Leave no one behind.

He had broken it. He had broken it with the one person who really mattered to him, the one person who had truly trusted him. He had saved, or at least tried to save, everyone else in the past, whether he knew them or not.

In a way it was her fault. If she had been captured three years before she was, before he had become so close to her, he would have gone back for her straightaway – or he wouldn't have left without her at all. However, working so closely with her over the years, he saw how much Atlantis meant to her and that she would happily give her life ten times over to protect it and her people. So he put the city before her. He had never felt more conflicted before or since.

Sheppard walked to the door and it opened. It had been some hours since the party had begun and it was still only three o'clock in the afternoon. But after all they had been through, today had been declared as a day off and so the celebration would probably go on for a good while yet. John had had more than enough. Looking around, he noted that everyone seemed to be occupied and made a beeline for the exit.

He reached the transporter booth and breathed a sigh of relief as he activated the sensor to open the doors.

"You aren't staying?"

John inwardly shuddered. Teyla, of course. Who else would it be but the one person he couldn't bear to face? He didn't turn around.

"I…I'm tired," he stuttered.

"It is still early in the day," Teyla countered.

"Yeah, but this party's gonna go for a long while yet. Figured I'd take a nap and come back fresh." He went to enter the transporter, praying she would say nothing else.

"John, we must talk," she said gently.

Sheppard stopped before he entered the booth and his head dropped. "There's nothing to talk about."

"Please, John."

Sheppard slowly turned around to face her. "Look, Teyla, I am really sorry about yesterday. I was tired and I should never have unloaded on you like that." He looked into her eyes unflinchingly and lowered his voice. "But let's get one thing clear: we are _never_ going to talk about it again." With that he turned, walked into the transporter and selected his destination, making sure the doors were closed before he slumped against the wall.


	5. Chapter 5

**Chapter 5**

The man in front of the Stargate wore an almost irritating all-knowing smile, a smile which suggested a wisdom and superiority those around him would lack. Elizabeth took some solace in the fact that if he was truly an Ascended Ancient he may indeed have something worthy to say.

Rodney was the first one to break the tense silence as he joined John and Elizabeth on the Gate Room floor. "Janus? The Ancient scientist?"

Of course Elizabeth knew the name the moment he had spoken it. The encounter with the more than ten thousand year old version of herself was still fresh in her mind, despite the fact they had met her five years ago. It was thanks to Janus that the elder Elizabeth was able to stay in Atlantis and prepare it for the arrival of the Expedition, making sure they did not suffer the same fate as occurred in the original timeline.

Of course, she had never met Janus herself. So how could she be sure he was who he claimed?

John, unsurprisingly, had the same thought. "And you can prove that?"

Janus ignored John and spoke directly to Elizabeth. "I am with you right now."

Elizabeth, Rodney and John all exchanged confused glances. Elizabeth stepped out from behind John, positioning herself between the two men. "Excuse me?" she asked, trying to keep the scepticism from her voice.

Janus looked around the Gate Room, then at the soldiers still pointing their weapons at him and at Sheppard and McKay. Finally, his attention returned to Elizabeth. "Why are you here?"

Rodney turned to the others and whispered, "Is there anything in the reports that says Ascension makes you crazy?" However, even his lowered tone was fairly loud and Janus chuckled, good-naturedly.

Again, he directed his words to Elizabeth. "Doctor McKay, I take it?"

Elizabeth looked at Rodney. "Yes."

McKay looked to Sheppard. "I'm right here, aren't I?" he said irritably.

John released an exaggerated sigh. "Yes, you are." McKay glared at him.

"He is just as you described him," Janus said.

"Hey!" snapped Rodney. "_He_ is standing right here!"

Elizabeth placed a hand on Rodney's shoulder in an attempt to placate him. McKay turned to her with his eyes wide and his mouth open ready to complain further. She shook her head slightly. He clamped his mouth shut.

She turned back to Janus and took a step forward. "May I ask why you're here?"

"I told you, Doctor Weir," answered the Ancient. "I have a proposition for you."

Elizabeth decided to play along. "And what exactly are you proposing?"

Janus grinned again. "Ascension."

John moved forward to stand beside her. "Well, thanks for the offer but we're just fine on this plane of existence." He still had his gun in his left hand, although it was now lowered, but she felt his other hand hover at the small of her back protectively.

Janus, once again, addressed Elizabeth. "You know that I was only referring to you." He paused, even as John stepped between him and Elizabeth. "And you know why."

John moved back to her side and she saw it in his eyes. They both remembered the conversation earlier. Something wasn't right.

And then she realised what it was. It was everything. She looked up to the Stargate and then scanned the Gate Room, Control Room and all the people. None of it was real. She wasn't even real.

Her eyes finally rested on John. The illusion was broken again. But as the people around her started to disappear she gazed into his eyes. She didn't want him to go. She could see the sadness within them. Then he was gone.

The Gate Room was empty now, apart from herself and Janus. She glared as she walked up to him. "Why did you do that?" she said loudly. "It was working until you came along."

"It wasn't real," explained Janus.

"So what?" Elizabeth shot back. "It was better than reality."

Janus spoke in calm, even tone. "What about Ascension?"

"I thought you would know, given your omniscient status." She paused, noting how much she sounded like Rodney McKay. "I'm a Replicator. I can't Ascend. I already tried." She bowed her head in shame.

"Mmmm."

Elizabeth looked up. "What?"

"You're not a Replicator."

"Excuse me?" She almost felt insulted, but she did not know why.

"I saw you and the others. You are not like them."

"I don't understand." She was just confused now and Janus was talking to her as though she were a five-year-old child.

"You didn't answer my question," he said to her.

"What question?"

"Why are you here?"

"Because it's safe."

"Safe?"

"If I'm here I don't know where I really am or the things that led to me being there." She sighed heavily. "If I'm here it doesn't kill me."

"Exactly." He pointed a finger at her gleefully.

"What's that supposed to mean?" After what she had just told him she did not expect that short, yet strange response.

Janus put his hands on Elizabeth's shoulders and squeezed them gently. Comforted by the contact, she looked up at him to see his eyes wide with excitement. "There is a reason it causes you such pain. Your body may be lost but not your…what would you call it? Your soul? Do you understand?"

"What are you saying?" Elizabeth asked incredulously. "My soul… is that what this is?" She used her arm to indicate the Gate Room. "It wasn't destroyed?" It really felt like it had been.

"Your soul is who you are. It will be changed by its experiences. It may be perverted but a soul is only lost from this existence by death." Janus grinned again. "And you are not dead, Elizabeth."

Elizabeth opened her mouth to speak but stopped as she felt her eyes well up. Her soul was intact. Despite all it had been through it – she – was still alive. It made sense of course. She still felt pain, love, loss, regret. But to be told that she was not merely an echo, that she was truly Elizabeth Weir gave her an almost tangible feeling of peace.

However, despite the joy, she still had questions. "But I tried to Ascend before. Why didn't it work?"

"I would have thought that was obvious," answered Janus. "To Ascend you must throw off the shackles of this life, of all that has happened and all that could have happened. If you are not able to do this completely then Ascension could not be achieved."

"But I did that!" cried Elizabeth.

"Did you?" Janus looked around the room. "Did you truly let all of this go? Let go of all the possibilities?"

She pondered his words. She had worked hard with the other Replicators to achieve the inner peace required for Ascension. She knew what to do after all her research on Atlantis. But she had been through so much, had lost everything. Was Janus right? Was her failure to Ascend down to her inability to let go of her past, her hopes, her future?

She took a step back and turned away from the person in front of her. He was offering a way out. A way to escape this interminable hell, trapped in a body not her own, languishing in dead space.

Did she deserve it though? After what she had done on her return to the place she once thought of as home, to the people she once saw as her family? Or had she suffered enough?

She turned back to Janus. "Can you help me?"

Janus nodded. "I believe I can."

Elizabeth let out a breath. "How?"

"I think the first thing you must do is come to terms with how you came to be a Replicator."

Elizabeth chuckled humourlessly. "And how do I come to terms with that? And everything that came after?"

Janus put his hand out to her. "Show me."

She looked at his hand, hesitantly. Show him? What did he mean? She thought she knew but shuddered at the implication. Could she allow herself to relive the events that led to this? The idea terrified her.

Without looking away from the hand, she whispered, "I'm scared."

Janus answered, his voice soft and soothing. "That just means you're alive."

She bit her lower lip as she reached out towards him. She_ was_ scared but she knew she had to do this. She had to confront the terrors of her past. How could she move beyond them if she did not? She took a deep breath and held it as she closed the gap between them, gripped his hand tightly and closed her eyes.

* * *

The Gate Room was darker when Elizabeth opened her eyes again. She could feel the floor beneath her feet rumbling. Janus was beside her, still holding her hand. The Control Room staff was moving towards the stairs to their workspaces and she could hear Rodney shouting. Realising what she was witnessing she turned to the stained glass windows by the balcony to see _herself_ gazing out in wonder as the city rose up from the ocean. She gasped and tightened her grip on her companion's hand as the sky outside glowed red and the windows shattered. She saw herself thrown back by the force of the blast and spun away, tears streaming down her face.

"So this is where it all began," commented Janus, almost casually.

* * *

She shut her eyes, unable to watch herself sitting in the isolation room in a hospital gown with Teyla talking to her in an orange quarantine suit, as she was scanned by Doctor Keller who was also suited up. Teyla was telling her that she was glad she was alive. Elizabeth was telling her that it was a bad idea.

How prophetic. Janus watched with great interest. "So, in order to save your life they activated the inert nanites in your bloodstream?"

Elizabeth nodded. "I was unconscious at the time, dying. If they had been able to ask me I would never have let them do it. It was too dangerous."

Janus looked at her quizzically. "You would have rather died than…?"

"Become part-Replicator?" Elizabeth finished. "Absolutely."

"Why did they do it then?" asked Janus.

She sighed. "I suppose they didn't want me to go."

"I see."

* * *

This time they were in the same room and Elizabeth was surrounded by John's team, being asked about joining them to steal a ZPM from the Replicator homeworld. Elizabeth noticed the intensely sad eyes as John watched her, she didn't see that the first time round.

Elizabeth then told John not to hesitate to use the kill switch that had been built into her nanites if it became necessary. John tried to tell her that wasn't going to happen.

* * *

Elizabeth had Oberoth on his knees. But she could see herself weakening. Oberoth succeeded in breaking her connection to him just as John and Ronon arrived. Elizabeth sobbed quietly, eyes squeezed shut, trying not to hear.

"Elizabeth." John's voice was calm but she could sense the urgency.

"Get to the jumper." She sounded more urgent.

"You're coming with us."

She heard a shot, knew that was when Oberoth was hit with an ARG that failed to work.

"I can't keep them frozen much longer!" she cried.

"We're not leaving you behind," he said, his voice firm.

"If you don't leave right now, none of us will get out of here, so go! That's an order!"

She heard Ronon shout as the firing began. "Come on!"

He called to her. "Elizabeth!"

"GO!" she yelled.

She opened her eyes to see herself being surrounded by Replicators with no hope of escape.

* * *

She was sitting on the floor of a cell, identical to the one on Atlantis, fortified by horizontal bars and a forcefield. She appeared to be catatonic.

Elizabeth looked down at her. "Get up," she whispered. "Do something."

She watched Oberoth enter the room and then the cell, along with two others.

"You will tell me where they are." He spoke matter-of-factly.

Elizabeth watched her other self smile. "No." She still believed in the power of words at this point.

"Tell me or suffer the consequences."

She saw herself get up, square her shoulders and look Oberoth in the eyes. "Do what you must, Oberoth, but nothing you do to me will get you what you want."

She was pushed to her knees by Oberoth's subordinates and she could see his sneer as he pushed his hand into her forehead.

* * *

Oberoth retracted his hand seconds later as the door to the brig opened. Four Replicators entered, the first two dragging an unconscious John Sheppard, the other two with Ronon, also unconscious. They were unceremoniously dropped onto the floor of the cell.

Janus and Elizabeth watched as she crawled quickly to John, checking for a pulse. He stirred and opened his eyes. He saw her and put his hand up to her cheek. Tears streamed down her face as they moved closer to each other, lips almost touching –

She stopped and stood up. Facing Oberoth, her expression became resolute. "You'll have to do better than this," she declared defiantly, without a trace of the fear that she was feeling. "I know they got away, I could tell from the way you all reacted and I know I won't see Atlantis again."

She fell forward as Oberoth's hand came out of her head and they were back in reality – well, the reality Janus and Elizabeth were observing.

"On the contrary, Doctor Weir," Oberoth said darkly. "You will see Atlantis again – sooner than you think." With that he thrust his hand forward again with extreme force, causing her to cry out in pain.

* * *

They were in the Infirmary on Atlantis. John, Rodney, Ronon, Teyla and Doctor Keller stood around a bed. Janus and Elizabeth looked closer to see the other Elizabeth – Weir – was in the bed.

"It's a good thing we got you out when we did," said McKay. "They were obviously looking at reprogramming your nanites." He smiled smugly. "Thankfully, I was able to neutralise them."

Weir looked shocked. "I thought they were keeping me alive."

"Yes, they were," said McKay. "But they were able to repair your injuries so _I _ have rendered them inert again."

John kept watching Elizabeth as he responded to McKay. "Does that mean he's human again?"

He sounded even more pleased with himself as he said, "Yes, it does."

John surreptitiously stroked Weir's arm with his forefinger. Elizabeth and Janus seemed to be the only ones who noticed.

"How did you find me?" Weir asked.

John answered. "We came back once the ZPM was installed with Teyla and Keller. McKay was able to rig a Life Signs Detector to scan for you and we found you in the cell. Oberoth had his hand in your head."

"We think he was trying to get your nanites to replicate," Rodney put in.

John glared at McKay but continued. "Ronon took him out and I grabbed you but you had passed out. Then we got out of there as quickly as we could.

Weir looked at all of them. "Thank you so much." Elizabeth, observing this, felt a wave of nausea.

Weir started to look pale. "Ooh," she said quietly as she put her hand to her chest.

"Elizabeth," said Keller, "Are you all right?"

"My chest hurts," Weir said. She leaned forward and let out a moan.

"Help me get her to the scanner," barked Keller.

Ronon picked her up from the bed and jogged over to the scanner, laying her on the table. The others followed.

The green laser grid activated and passed down her body. As it reached her chest, Keller, viewing the screen, gasped.

"What is it?" said McKay, joining her at the monitor. "Oh, no."

"What?" growled Ronon.

Elizabeth saw John take Weir's hand as she double over in agony. _Please don't let this happen again, _she thought.

"The nanites…" said Rodney, "they're active and they've…they've turned her."

John turned back. "Are you saying she's a Replicator?" he demanded, though he didn't let go of her as she cried.

"Worse than that," said Rodney. "She's a Trojan Horse!"

"A what?" said Ronon.

"The nanites turned her body into a bomb!"

John looked down at her. "How do we fix her?"

"We can't fix her!" shouted Rodney. "It's too late!"

Weir sat up and screamed. As she did her body seemed to glow red. The light grew brighter until she was completely lost. Her body then exploded as the red light shot out in all directions, enveloping everyone and everything.

* * *

It was the beginning of the torture.


	6. Chapter 6

**Chapter 6**

John slumped back into his chair, completely exhausted. The debriefing had taken four hours. He looked across the long table at his 'interrogators', namely Generals Jack O'Neill and Hank Landry and Mr Coolidge from the IOA. The Generals were whispering to each other, while Coolidge was writing _a lot_.

Overall, the debriefing had been fairly straightforward. The hard part – for Coolidge anyway – was John's decision to take his nuclear missile-equipped F302 up to the Hive ship – something he did without prior permission. Coolidge seemed to be very unhappy that he had disobeyed the order to return to the SGC and, well, have an idea of his own. The two military officers didn't seem to have a problem with it. Quite honestly, Sheppard was surprised that Landry was taking it in his stride given that John had flagrantly flouted his orders in the past.

There really was not that much for Coolidge to complain about anyway. If the nuclear weapon hadn't been brought on board the Hive it would not have been destroyed. Earth could have conquered by now – only four days after its arrival. So, as far as Sheppard was concerned, that line of questioning was moot. O'Neill obviously thought so as well, given that he told Coolidge to stop after forty-five minutes of him asking the question, why did you disobey a direct order? Or any questions related to it.

General O'Neill looked over at him. "Okay, I think we're done here."

"Does that mean I can go?" asked Sheppard, trying not to sound excited or relieved at the prospect.

O'Neill nodded. "Unless you have any questions for us?" He didn't mean it. Debriefings only ran in one direction.

John went to get up but stopped. He was about to break the unspoken rule of the military debriefing, but the General did open it up to him. "Actually, I do have a couple of questions, if you don't mind, Sirs."

Coolidge's head snapped up, whilst the two Air Force officers looked confused. "Umm… okay?" said O'Neill.

Sheppard leaned forward in his chair, placing his forearms on the table and clasping his hands. "What's going to happen to Todd?"

Coolidge started going back thorough his reams of notes. Landry took the silence to ask, "Todd… the Wraith?"

Sheppard nodded but did not speak.

O'Neill leaned forward, mirroring Sheppard's position. "He's going to take an all-expenses paid trip to the SGC, until Area 51 is up and running again. And we'll be asking him some questions."

Sheppard nodded again. "You know that he – "

"Feeds on people? Yes, we're aware of that."

"He may be willing to assist in Doctor Keller's work to stop the Wraith feeding on humans. He helped before."

"And he's screwed you over more than once, right?"

"True."

O'Neill leaned even closer. "Do you want to have a talk with him? Say goodbye?"

Sheppard heard the sarcasm but shook his head vigorously anyway. "No thank you, Sir. I'll be more than happy to have one less pain in my ass around." He looked to Coolidge, realising his comment may be seen as inappropriate. "No offence."

Coolidge didn't reply. There was silence.

"Okay, next question." John shifted in his chair again. "What about Atlantis? Long term, I mean."

Jack nodded this time but before he could reply Coolidge piped up. "What do you mean?"

John sighed. He was certain that General O'Neil understood his query. "Well, what's the plan for Atlantis after the repairs are complete? It can't stay where it is."

Coolidge smirked. "Of course it can't stay in San Francisco. But there is a lot of ocean on planet Earth."

"And a lot of boats on those oceans!" O'Neill put in.

Coolidge seemed to think, then nodded finally, conceding the point. "I suppose it would be difficult to keep a floating city secret. Even an invisible one."

His face then lit up. "But there must be plenty of planets here in the Milky Way that have oceans."

O'Neill appeared to enjoy raining on his parade. "That are uninhabited and don't have a Stargate?" John kept his face straight but inwardly laughed at his defiance of Coolidge and, by extension, the IOA.

John took a deep breath. It was now or never. "Permission to speak freely, Generals?"

"I think you already are," said Landry. His expression softened – slightly. "But go ahead."

"The best idea might be to go back to Pegasus."

The tension that followed his statement was broken by a short, incredulous laugh from Coolidge. The other two looked at him. His smile faded as they stared. "Well, we can't do that," he told them, rather than Sheppard. He then turned back to John. "Why should we do that?"

John looked to the two Generals to answer. "We came here to help Earth against the Wraith. And we did that. But we left a galaxy of people still living with the Wraith and Atlantis is their best hope. Atlantis belongs in Pegasus."

Coolidge shook his head and his hands wildly as he spoke. "No, we need Atlantis. May I remind you that Earth lost its only planetary defence when the Wraith attacked Area 51and destroyed the Ancient control chair. Atlantis is now our only defence!"

"But you already agreed that Atlantis can't stay on Earth." John stopped himself from rising from his chair as he spoke.

Coolidge, however, was almost shouting. "I don't - !"

O'Neill shot up out of his seat. "Okay!" he said, cutting of Coolidge. "Look, Colonel, the truth is, it hasn't been decided yet."

"Yes, Sir," he said quietly. "Can I ask that you consider one thing though?"

"What?"

"What the Expedition members think. You know, we were there for five years, our opinions should count for something."

Coolidge opened his mouth to argue, but O'Neill silenced him with a raised finger.

And then O'Neill surprised Sheppard. He smiled. He realised then that, of anyone on Earth, this man would be the one who understood the responsibilities Atlantis had left behind. "We will. Thank you, Colonel." He reached across the table and John stood to take the offered hand. He then saluted. Both Generals saluted as well. "Dismissed."

As John left the room, he knew what he had to do.

* * *

John was beamed into the Atlantis Gate Room to be greeted by Woolsey and McKay.

"So," Rodney asked nervously, "how did it go?"

"It was okay." John shrugged, nonchalantly.

"What, that's it?" McKay folded his arms, then unfolded them, clearly agitated. "You've been gone for hours!"

"How was Coolidge?" Woolsey asked more calmly.

"Unpleasant." John leaned towards Woolsey, as if to tell him a secret. "He doesn't like me."

"Oh?" Woolsey sighed. "What did you do?"

John reeled off the list, his fingers counting each one, "I disobeyed a direct order, I asked questions at the end of the debriefing and… I may have… said that we should take Atlantis back to Pegasus."

"You what?" yelled Woolsey.

"Really?" McKay sounded stunned.

John looked at each of them. "You don't agree?"

"I do agree." Rodney was quick to respond. Woolsey said nothing.

There was an awkward silence.

"So… how are the repairs going, McKay?" _Get Rodney talking, break the silence._

"Slowly." McKay started walking down the corridor out of the Gate Room, beckoning Sheppard to follow.

Sheppard nodded to Woolsey and went after the scientist.

"We've taken two of the three ZedPMs off-line as we only need one to power the cloak. Parts of the city were damaged on entry into the atmosphere. Amazingly, the shield was able to protect a majority of the systems. But the star drive is by far the most damaged system and fixing it is going to take time as I have to send people underwater. So you really think we should go back?"

John blinked at the swift change of subject but went with the flow. "It's the right thing to do. The Wraith are still a big threat and Atlantis belongs there."

Rodney nodded. "So you wouldn't want to stay then?"

John stopped walking. Rodney had taken a few steps when he realised he was alone. He turned back. "What?"

"Do you want to stay?" John asked.

McKay stumbled over his words. "Well…I mean…not forever, but for a while, yeah." He squared his shoulders and spoke more confidently. "I want to spend some time with Jeannie and also… Jennifer… she wants me to meet her father."

"Wow," said John, leaning back against the wall in the corridor. "Big step."

Rodney slouched against the same wall and gulped. "Huge."

"Nervous?"

"What do you think?"

"You'll be fine."

They stayed quiet for a few moments before John spoke again. "Would you do something for me?"

"Sure."

"General O'Neill says he'll take into account the Expedition's opinions on what should happen to Atlantis. Could you make sure everyone says what they think at their debriefing?"

"Well, I'm pretty busy with the repairs and everything," McKay said. "Why can't you do it?"

"Because," said John, pushing himself off the wall, "I have been told to take a few days off. So I am going to see my brother."

"What? Why do you get to go?"

"Relax, Rodney," said John, sighing. "Everyone's going to get time off after their debriefing."

"Oh. Okay then."

"Look, I'll talk with Lorne and Ronon before I go and they can spread it around the military contingent. If you could talk to the civilians, I'd appreciate it."

Rodney huffed and finally acquiesced. "So, when are you leaving?"

"Right now."

"Well, see you later then." Rodney was looking down the corridor.

John put his hands in his pockets and looked at the floor. "Yeah… see you later." He was surprised when Rodney's hand came into his line of vision. Looking up, he saw his friend's apprehension. John took his hand and shook it. They broke off at the same time.

After another few moments of looking everywhere but at each other, John left. As he walked away, he felt his brain kick back in to gear. He had spent most of the day answering questions and pondering the quandary of how to get the Powers That Be to allow Atlantis to return to Pegasus. It had been a welcome distraction. He didn't particularly want to leave Atlantis but, he had to admit that a change of scenery might do him the world of good. Since Atlantis had returned to Earth, he had a hard time keeping his thoughts and regrets regarding Elizabeth out of his mind. Before all of this, he had found a way to keep going by simply not allowing himself to ever think about her. It wasn't ideal and, according to Teyla, his friends had noticed a change in him, but it enabled him to do his job. Now there was nothing for him to do to keep the thoughts away.

Visiting Dave and his family could give him that something that would help divert his attention. But before he could see them he had an important task to take care of.

* * *

Sitting in the car at the end of the street, John Sheppard took out the SGC-issued mobile phone and dialled the number that would be forever carved into his heart.

It was something of a ritual now. Whenever he was on Earth he would give her a call. They would make small talk, there would be a brief mention of Elizabeth, she would ask him to come and visit the next time he was in the area and he would promise he would try.

After the first and only time he had visited her, John had vowed he would never go there again. It had been so devastating, talking to her about Elizabeth, seeing the same green eyes he had so often got lost in. But he felt that Elizabeth would want him to make sure she was all right and make sure that she knew he was there if she ever needed anything.

"Hello?"

"Hi, Mrs Weir, it's John Sheppard."

"John, it's good to hear from you." Mrs Weir sounded like she was in a good mood today. John smiled at the tone, and again put aside his curiosity about the slight exotic tinge to her accent. "Are you well?"

"I'm fine, thanks. How are you?"

"I am quite well actually."

"You sound great," John said. "Is there something you're not telling me?" he gently teased.

"That's none of your business, Lieutenant Colonel," Mrs Weir said, obviously joking as well.

"Would you tell me what was going on if I told you I was a full bird Colonel now?" John responded.

There was a small gasp at the end of the line. John shut his eyes as an image of Elizabeth making the same sound invaded for a brief moment. "You've been promoted? That's wonderful. Congratulations, John!" Her words were warm and genuine. "Well, if you must know, an old friend of mine has come into town and he's picking me up shortly."

"Sounds like you have a hot date."

"Don't be so ridiculous!"

"No, it's fine," laughed John, "just make sure you're home by eleven!"

They both laughed for a moment but an awkward silence took over.

Mrs Weir was the one who broke it. "His son and Elizabeth went to school together." And there it was.

"Hard to imagine Elizabeth as a schoolgirl," John said quietly.

"When you visit I can show you some pictures."

John cleared his throat. "That would be nice." He tried to sound better than he felt.

"When Elizabeth was fifteen she had a terrible crush on Jordan – my friend's son. She was quite hard to live with at the time." Her voice was so sad.

John felt a lump in his throat. He gulped, trying to push it down before he spoke again. "Mrs Weir, I –"

She interrupted him. "It's all right, John. I know you won't make it this time, but promise me you will come soon."

"I'll try."

"Have you had any luck finding the watch?"

"Um…no, still haven't found it."

"All right."

He cleared his throat again. "Well, I should go."

"Of course, it was nice to hear from you, John."

"Goodbye, Mrs Weir."

"Goodbye."

He cut the connection, threw the phone on the passenger seat and rested his forehead on the steering wheel. These conversations always took so much out of him. It disturbed him how easy he found it to talk to her, to tease her and yet she always responded in kind. Just like her daughter.

After five minutes, John pulled himself together and started the car. He drove down the street and turned into the long drive. He parked up at the end of the drive in front of the huge house. Getting out, he took a deep breath of fresh air and looked across the fields to see two horses grazing in the afternoon sun.

John stretched and rolled up the sleeves of his white shirt. He walked up the steps and knocked on the heavy oak door.

He waited a few moments, patiently. It was a big house; it might take a while for someone to answer.

The door opened to reveal David. He was dressed in a pair of faded jeans and a white T-shirt with grease marks on it. Despite being two years younger than John, he had a smile that made him look far more youthful. "John!"

"I'm sorry," said John. "Did I interrupt a calendar photo shoot?"

Dave put his hand out and John took it to shake. Dave pulled him in for a hug, slapping him on the back with his other hand. A shocked John awkwardly put his free hand on his brother's back. He wasn't expecting this.

He pulled back and saw the huge grin on Dave's face directed to his chest. He looked down to see the front of his white shirt covered in black oil. "Oh, man!"

Dave laughed heartily. "I was working on the Mustang!"

"What, _in the house?"_ moaned John, still looking at his ruined shirt.

"Come on in." Dave walked back inside, leaving the door open. John followed, shutting it behind him.

Dave led him down the oak panelled hall into the rear kitchen. John sat on one of the stools of the central island whilst Dave picked up a full coffee pot from the main counter, along with, along with two mugs. He brought them to the island and filled the mugs, passing one to John. John took the sugar bowl and added two cubes.

"So," started Dave, "what's happening?"

John shrugged. "Not much, got a few days leave. Where are Martha and the boys?"

"Oh, they've gone to see her folks for a couple of days." He sighed. "They left yesterday."

John smiled humourlessly. "You, miss 'em, huh?"

"Always do," admitted Dave. "I just can't get used to the place without them around." Dave seemed to be studying him closely. Discomfort at the attention forced John to look down at the contents of his mug.

"You look tired, John."

"I'm okay." He still didn't look up. "So, what's up with the Mustang?"

They spent the next hour chatting about nothing in particular. John listened to his brother's stories about the trouble his nephews could get themselves into and the trip to Europe that was being planned for next summer. It was all so… normal. God, how he had wanted this. He hated it, but he envied his brother for having what he could never have.

John started when his brother put his mug down on the counter harder than was necessary. "Dave?"

"What's going on, John?"

"Sorry?"

"Look, I know we've only been talking again for the last year or so, but I think I know you pretty well. You're not the cocky bastard who walked out that door six years ago. What happened?"

John shrugged again. "Time passed. I got a great opportunity but it was dangerous. People were lost." He left it there.

"But," Dave spoke carefully, "you're in the military. You've lost people before. Why is this different?"

"Because I'm in command," answered John. He took a deep breath. "Because people died… or were taken by the enemy. Because I left someone behind." He lowered his head in shame. Tears formed but he stopped them from falling.

"Who was she?"

John's head came back up again. "How…? She… was a friend."

"Why did you leave her?"

"She ordered me to." In response to Dave's raised eyebrows, "She was my boss."

"So, where is she?"

"What do you mean?"

"You said you left her behind. So I take it she's not dead."

"No." John gulped. "But she may as well be."

"You know where she is?"

John was getting all twisted around. Why was Dave pushing him? This was worse than the debriefing two days ago. He had been vulnerable when he spoke to Teyla. Damn, he should never have spoken to Elizabeth's mother before he came here.

Then Dave said something that was a complete shock to him. "So, why don't you go get her?"

John got up and slammed the island top. "It's not that simple!"

"Why not?" Dave didn't even seem nervous.

"I can't say! But I would be disobeying orders for starters!"

Dave took a sip of coffee and nodded. "So?"

John was about to shout when he shut his mouth and leaned on the island. "What do you mean?"

"Come on, John," said Dave in frustration. "You know very well what I mean. You were nearly kicked out of the Air Force because you disobeyed orders and went after a friend. You told Dad that you didn't regret it and you would do it again in a heartbeat. You've always gone for what you wanted. Hell, you joined the Air Force in the first place 'cos it was what you wanted, even though Dad threatened to cut you off. Why is she different?"

John exhaled and spoke softly, resigned. "Her situation is different. It could be dangerous for everyone."

"Can you do anything to change that?"

"Change it?"

Dave took a deep breath. "Do you remember coming to visit us before your last tour in Afghanistan?"

John nodded.

"There was a kid here who liked to help with the horses at the weekend. Fourteen years old, his name was Stewart."

"Oh, yeah, he was a great kid." John smiled slightly at the memory.

"You and he became pretty close. He ended up telling you how he was being bullied and beaten up because of his speech impediment."

John waited for Dave to continue, unsure as to where he was going with this.

"Stewart was coming to the stables for months and we all knew something was wrong but he never opened up to us. You were there for five minutes and he told you everything. And then you taught him some self-defence and boxing over the weeks you were around."

"Okay," John said. "Is there a point?"

"A couple of weeks after you left he came to see me and told me that the one who was hurting him tried again and he stopped him. Gave him a nosebleed too." Dave smiled proudly.

"That's great. Why didn't you tell me?"

"Oh, well, I didn't get to. You came back, had your fight with Dad and I didn't see you again for four years."

John flinched at those words.

"Sorry," Dave said, "that wasn't supposed to sound so sarcastic." He shook his head. "Anyway, you changed Stewart's life."

"How?"

"He's an MMA fighter now."

"Really?"

"No!" Dave chuckled. "But no one ever tried to mess with him again."

"Cool."

"It's what you do, John. You see a situation you don't like and you look at the ways you can change it. So… can you do anything to change her situation?"

John shook his head. "I don't think so." He closed his eyes again as the image of F.R.A.N came forth. _Human bodies_.

John abruptly looked up at Dave. "I have to go."

Dave smiled knowingly. "Of course you do."

John walked quickly to the front door and opened it. He turned around to find his brother there. He put his hands on his shoulders. "Thank you."

Dave just smiled. He watched as his older brother ran to his car.

John got in the car and drove quickly down the drive. He had to get back.

As he reached the end of the drive, he hit the brakes. He looked to the left, then the right. As he scanned the road for traffic, doubt crept into his thoughts.

Was this a good idea? Was it the right thing to do? She had been gone for so long. As he worried, Dave came into his mind, a man so happy to have his family he missed the sounds of them in his home. Mrs Weir, a wonderful woman who missed her daughter terribly. Stewart, a boy whose situation so angered John he sought to change it.

John put his foot on the accelerator and turned left. He had made his decision and there was no chance he was going to change his mind.


	7. Chapter 7

**A/N:** Hi everyone. Thanks for continuing to read. Kicking it a little differently as this follows straight from the last one. But this chapter was a harder one to write. The reviews, however, have been really great and do keep me going. Anyway, I hope you enjoy this one.

**Chapter 7**

John had spent the long overnight drive considering all the possible implications and drawbacks of his hastily formulated plan. There were obstacles, a lot of them, and he needed to think of ways to deal with them.

The first problem was getting back to the Pegasus Galaxy, preferably with Atlantis. He had already taken steps that would hopefully resolve that situation soon enough.

However, at this moment he had a more pressing concern. How was he going to get authorisation for this mission? There were so many risks involved, so much which could go wrong. He was certain the IOA would never approve it.

John had considered not asking anyone and going ahead with the plan anyway. He eventually decided to call that 'Plan B'. There was still one option. If the IOA could not see the benefits perhaps he could convince a certain cavalier Air Force General.

With that at the forefront of his mind, John pulled into the car park of the Cheyenne Mountain facility. He looked at his watch. It was 07:00 hours. The General was still here for debriefing sessions but those would not start for two hours. He needed to see him before that.

John got out of the car and headed inside. After being cleared by security, he took the long lift ride down to Stargate Command beneath N.O.R.A.D. He then went to the locker room deciding it best to shower and change before doing anything else.

As the hot water cascaded over him, fear began to grip him. What would he do if he couldn't get the mission authorised? _It doesn't matter,_ he thought. He was going to find her, no matter what. He was ready to do anything.

But what if the mission wasn't allowed? What if it was? What about when they found her? Could she turn against them? Could she have gone crazy?

_Will she forgive me?_

John's forehead came to rest on the tiled wall below the showerhead as the full impact of that thought sunk in. What right did he have to assume that he would save her and everything would go back to the way it was before? The Powers That Be would never allow her to re-take command of Atlantis. They probably wouldn't even let her stay on Atlantis.

As for their relationship? He had never told her how he felt. Did he honestly think that she would wake up in the puddle jumper, see him and fall into his arms? It was highly unlikely. He had abandoned her twice. He would be lucky to get a punch in the gut and the silent treatment for the rest of his life. It was the least he deserved.

"Come on, John, that's not the point anyway," he said aloud. "You're doing this because it's the right thing to do."

John pushed away from the wall, his resolve once again strengthened and quickly finished his shower, dried up and put on a pair of black jeans and a black long sleeved T-shirt, taken from his overnight bag.

He made his way to the Briefing Room, certain the man he was looking for would be here or in General Landry's office next door.

However, both rooms were empty. Where else could he be? The commissary sprang to mind. Sheppard started to head towards the door when he heard footfalls on the metal steps leading from the Control Room up to the Briefing Room. He looked around to see Sergeant Walter Harriman entering the room, seemingly lost in the file he was holding.

"Hey, Walter," John said informally.

"Colonel." Walter didn't even look up or stop walking.

"Have you seen General O'Neill?"

"Try Doctor Jackson's office," Walter answered as he passed John.

"Thanks!" he called after the smaller man as he left the room.

Sheppard quickly found Doctor Daniel Jackson's office. The door, as always, was open. He looked in expecting to see two men somewhere amongst the clutter of computers, books, papers, chalkboards and artefacts. So he was surprised to find a neat stack of grey crates by the door and clean and bare table surfaces – and two men sitting on opposite sides of the main table in the middle of the room, drinking from white mugs. Probably coffee. Both were quiet and neither of them noticed his presence in the doorway.

Sheppard didn't know what was going on and felt as though he were intruding. Under normal circumstances, he would have left and found O'Neill later. _Oh, no you don't, John, _the voice in his head insisted. _You are doing this and you're doing it now!_ John gulped nervously. The circumstances were far from normal. He knocked on the doorframe.

General Jack O'Neill and Doctor Daniel Jackson both looked over.

"Colonel," O'Neill greeted him.

"Hi, John," Daniel jumped up from his stool and faced him. "What are you doing here?"

"Yes," followed O'Neill. "I told you not to come back for at least a week. It's been three days."

"Yes, Sir," said John. He gulped again. "But this couldn't wait."

Jack started drumming the table with his palms. John couldn't find the words so said nothing. _Hey, John, if you want to know an answer, you need to ask the damn question!_

Jack's hands came to a stop on the table top and he finally spoke. "Well, if it's about Atlantis, then you can stop worrying."

Sheppard narrowed his eyes. "What do you mean, Sir?"

"Atlantis is going back to Pegasus." He paused. "Ta-Dah!"

John breathed out, more than just relieved at the news. He was one step closer to getting Elizabeth back. "That's great. Thank you, General."

"Oh, don't thank me, Colonel." O'Neill shook his head, still grinning. At John's inquisitive raised eyebrow, he explained. "Well, after I debriefed the rest of your team I noticed a pattern forming. All of them said that Atlantis should go back. So I decided to make my life easier and take a…" He waved his hand, trying to find the right word.

"Census?" filled in Daniel.

"No."

"Poll?"

Jack snapped his fingers. "Yes! So I sent Sergeant Harriman over to Atlantis and he asked pretty much everyone -"

"No, everyone."

"Thank you, Daniel – _Everyone _what they wanted. Most of the Expedition –"

"Ninety-eight per cent."

"Yeah, ninety-eight per cent said they wanted Atlantis to return to the Pegasus Galaxy."

John was still confused. "And that was enough to convince the IOA?"

Daniel and Jack looked at each other. "Well… no," said Daniel.

"Nooo…" said Jack simultaneously.

"So…?"

"So," O'Neill said, "you need to thank Woolsey."

"Woolsey?" John uttered disbelievingly.

"I know!" said Jack. "But he gave the IOA a speech, telling them about the alliance or coalition you are involved with in Pegasus and that the best way to stop the Wraith getting here again is by defeating them there. It was quite moving."

"Wow," said John. Part of him was still having trouble processing the information he had just received. On the one hand, he was pleased that McKay, Ronon and Lorne had done what he had asked of them. They never let him down. But his brief discussion with Woolsey after his debriefing had left him with the definite impression that he didn't want Atlantis to return. Well, it didn't really matter now. With that matter over, John pushed ahead. "It's fantastic. But that's not why I'm here."

"Okay," said O'Neill, puzzled. "What's up?"

Sheppard looked at Jackson. He didn't really want to say it in front of anyone else, not yet anyway. He just needed to convince one man and an audience would not help. "I need to talk to you about a mission I need to carry out when we get back." He hesitated, looking at Daniel again. "It's a military mission."

Daniel took the glances in his direction as a hint. "I'm gonna get some more coffee." He quickly left.

General O'Neill indicated to the vacated stool opposite him. "Why do I get the feeling I'm not going to like this?"

John took a deep breath, summoning all the courage he could muster. He moved to the stool but, instead of sitting, he planted both hands on the table and leaned forward. He was fairly sure of how the General was going to react but he was determined. He knew that the man before him subscribed to the 'Leave no man behind' philosophy he lived by. He remembered Elizabeth telling him stories of the various scrapes SG-1 got into and the lengths Colonel O'Neill went to protect his team. He hoped he could appeal to this part of him.

_Now or never, John._ "I want to get Elizabeth Weir back, Sir."

Jack O'Neill spluttered as he quickly pulled his coffee mug away from his mouth.

_Okay, not the best first reaction,_ thought John, _but not the worst either._

O'Neill coughed, and then looked up, bewildered. "You're not serious, are you?" He coughed again.

"Completely," stated Sheppard.

O'Neill opened and closed his mouth several times in a passable impression of a goldfish. "Okay… and when you say you want to get Doctor Weir, you mean…"

"The Replicator we sent through the Stargate into space."

"Ah, I thought that's what you meant." O'Neill looked down and then back up at John. "I read the reports on that. Didn't you say that you couldn't be sure it was really her?"

"Actually," retorted John, "I said there was no physical evidence that she was or was not Elizabeth." He almost winced at the slip but carried on; hoping O'Neill didn't notice the use of her first name. "But she saved Atlantis that day and I believe that only Elizabeth Weir – our Elizabeth Weir – would have been willing to give up everything to do it. He leaned further forward. "It was her."

Jack's brow furrowed, the worry clear. "She's dangerous."

"We'll take precautions."

"She's a Replicator."

"She doesn't have to be."

"Huh? What?"

John finally sat down. He had his full attention and for the moment that was all he could ask for. But the plan he had devised so far was sketchy at best with a lot of catches. He just prayed that O'Neill wouldn't see that.

"Here's my plan," he started. "We take a puddle jumper through the Spacegate and we retrieve her, only her. We bring her to Atlantis. Then we put her in an isolated part of the city under guard and a force field along with a science team who will help her with her original idea of creating a human body. She transfers her consciousness into that body and we have Doctor Weir back." He sat back and waited.

General O'Neill was quiet. After a few moments John wanted to get up again and pace to release the nervous energy. He was so exhausted, having not slept for at least twenty-six hours but he was running on adrenaline. Or at least that was it felt like.

"Do you really think it can be done?"

He felt a small swell of hope as he heard the question. It was not a dismissal. "I think with Doctor Weir's knowledge from the Replicators, the research we have from Michael regarding Carson Beckett's cloning and Rodney McKay, it is possible." He made sure he sounded more confident than he felt. Getting her was relatively easy. They knew where she was and they had the means to get her back and revive her. However, in all his internal deliberations, Sheppard had desperately tried not to think about the possibility that they may not be able to create a suitable body for her. If that were the case, would he be ordered to destroy her? He knew that would be the likely outcome but he doubted he would be able to do it. He needed another plan to combat that eventuality. For the moment, though, he pushed that to the back of his mind and focused on the man in front of him.

"Why?" the General asked.

John almost laughed at the question but stopped himself. "Why do you think, Sir? We left her behind. I left her behind. What happened to her was not her fault and she deserves a chance."

Jack shook his head. "No, I mean, why now?"

"Oh," said John, scratching the back of his head, fruitlessly wishing he could erase that outburst from the conversation. "Honestly, Sir, I made the decision to do what I thought she would want me to do; take care of her city." He sighed heavily. "But she should have seen Atlantis' return to Earth. I should have done something sooner. I was wrong."

Jack cleared his throat before he spoke. "Look, John," he began sadly. "I understand what you're saying. I feel the same. But sometimes, there's just no other choice."

"But there is," John cut in, keeping his voice calm as he felt his heart slow with the disappointment.

"It's dangerous to bring a Replicator to Atlantis, even if you think it's someone you trusted."

John responded. "I don't think, I know."

O'Neill slammed his hand down on the table. "You can't know!"

John looked Jack in the eye and spoke quietly. "I can."

"How?"

He wasn't sure how to answer. He didn't want to tell his superior officer how he felt about Elizabeth but at the same time, the close relationship he had shared with her allowed him to see what others did not. "Well, she sacrificed herself and took the Replicators with her."

"And?"

John exhaled. The adrenaline rush was gone, replaced by almost paralysing dread. _He's not going to change his mind._ When he spoke again he could hear his nervousness coming through. "Before she went through the 'Gate, she looked at me. She knew what we were going to do and she wanted me to know she was okay with it."

"And you got all this when she…looked at you."

"Yes."

Silent tension filled the room as John watched O'Neill for any sign that he was going to come around. Unfortunately, all he could see was a distinct lack of belief in what he was hearing. John supposed he could understand that. After all, his last argument was hardly taken from a military standpoint.

_A military standpoint._ Maybe that was the way to fight for this. "All right. What about this?" He paused as he waited to make sure he had the General's interest again. "The Replicators are incredibly advanced machines, right?" O'Neill nodded his agreement. "Right now, eight of those incredibly advanced machines are floating in space where anyone could come across them." He pointed a finger at Jack for emphasis. "Maybe even the Wraith. We can't leave that kind of technology for the Wraith to find and if they found Doctor Weir they may be able to find a way of extracting information from her. Information about Atlantis...about Earth."

Understanding started to appear on Jack's face. "I see your point." He looked away. But when he looked back his expression was different. John couldn't pinpoint what he was seeing. That troubled him.

O'Neill spoke at last. "_If_ I were to authorise any mission, then it should be to destroy all the Replicators."

Sheppard jumped up before he had a chance to say anything more. "What?" he cried. No, it wasn't supposed to go this way. John licked his lips, trying to keep himself from openly panicking. _Destroy her?_ He couldn't destroy her, kill her. He loved her.

"It's too dangerous! You can't bring a Replicator to Atlantis!" Jack's voice was loud and firm but he was not shouting. "And you know that Doctor Weir would rather be destroyed than put Atlantis or Earth at risk."

John slumped back down on his stool. This was not going the way he had hoped at all. He couldn't do it. He would not sacrifice her again. Of course, O'Neill was right. Elizabeth would rather die than cause problems for Atlantis but this time it was his decision and he was not going to kill her. Not again.

Desperation was taking hold. The only thing that was working in his favour was that O'Neill was speaking hypothetically…for the moment. He had just saved the world! Why couldn't fate or destiny or life or whatever cut him a break? He decided to change tack again, wondering at the same time how General Jack O'Neill, United States Air Force General, would respond to blackmail.

"General," he said slowly. "I-I saved the world recently."

"I know this."

"Well," Sheppard continued, "don't you think that there should be some kind of reward for that?"

"Yes, it's called promotion, Colonel." He could hear that O'Neill's patience was wearing thin but he also knew he couldn't stop.

He laced his fingers together and placed them on the table. "You know the promotion doesn't mean anything, Sir."

"Hey!" said Jack. "Did you forget that around seven years ago you were almost dishonourably discharged? The fact that you're a Full Bird Colonel now is a minor miracle – at least!"

It was Sheppard's turn to hit the table in frustration. "Damn it!" He leaped up and turned away from O'Neill as he tried to collect himself. But he couldn't hold back his anger. He spun back around. "We don't leave our people behind!" he shouted, his arms flailing. "I left her behind twice, first, in the hands of the enemy and then in limbo! I don't deserve the promotion!" He slowed down and took a deep breath. He leaned on the table again. "I have to get her back. It's all because of her."

"What is?"

"I haven't forgotten what happened seven years ago. But six years ago I met someone. Someone who decided to trust me, to believe in me, without any good reason. If it weren't for her I probably would have quit the Air Force years ago. You're right. It is a miracle that I'm a Colonel now. Elizabeth Weir was that miracle."

* * *

Doctor Daniel Jackson stood outside his office wishing he could not hear the argument going on within. He really should have closed the door when he left. For that matter, he really could just go away and come back later.

However, once he realised what the debate was about he made the decision to stay.

Daniel had considered Elizabeth a good friend. She was an incredibly intelligent woman with a charm and charisma that could melt the harshest world leader's icy exterior. He had been very upset when he heard what happened to her. But to be left trapped in deep space? Daniel shuddered at the thought. She was a great person and she truly didn't deserve to have suffered that fate. He still held out hope that he would see her again one day though. She wasn't dead, after all.

He was brought out of his thoughts when the silence was broken once again by Sheppard.

"Anyway, I'm gonna get her whatever you say. So you may as well say yes." His voice was light but Daniel knew that he was serious.

"I could reassign you," was Jack's response.

"I'll find a way back, Sir. I can promise you that."

Daniel was hard pressed not to pump his fist in the air. How could Jack not allow Sheppard to save Weir? The passion and intensity he was expressing was contagious. The last time Daniel was on Atlantis, he was somewhat aware of how different John Sheppard was from the Major he had met in Antarctica. His whole demeanour went from cocky and fun to sombre and serious. Daniel was too busy at the time hunting for Janus' secret laboratory to pay any real attention to the changes and the reasons behind them. But this was the John Sheppard before those changes. Before everything seemed to get him down.

He heard Jack sigh. _Uh-oh_, Daniel thought. He couldn't do it. He could not stand by and say nothing. He couldn't let Jack say no.

Daniel squared his shoulders, stepped into the doorway and coughed to make his presence known before Jack could say anymore. "Sorry, I thought you would be done by now," he lied.

"Well, we're not," O'Neill said sternly.

"Yeah, I can see that," Daniel said. "By the way, I could hear you as I was coming down the hall."

"Oh," said Sheppard. He looked worried. Well, given the nature of what he was asking it was understandable that he would not want anyone overhearing.

Daniel took Sheppard's momentary distraction to look at Jack. _Just ask me what I think_, Daniel silently pleaded, hoping his best friend would get the message.

"Okay, fine!" cried O'Neill, flinging his hands up in the air. Daniel cringed as he saw Sheppard's face light up. "No, not you," Jack said to him. John's expression dropped again, and Daniel felt genuinely sorry for him. There was something in his eyes that reminded Daniel of the sadness and pain he felt when he lost Sha're to the Goa'uld. _Whoa,_ he thought, _could that be true?_

Jack continued to speak. "Daniel, you obviously have something to share, so share already."

Daniel walked over to the table. He took off his glasses and cleaned the lenses on his shirt tail, preparing himself to once again, disagree with Jack. "I didn't hear everything so I'm going to assume you have a plan for after you get Elizabeth back, John."

Jack glared. "He does."

"Okay." He put his glasses back on and looked at O'Neill. He chose his words carefully, knowing from past experience that when he and Jack disagreed it could get pretty heated. "You know, Jack, you were in stasis for three months and I worked with her every day while she ran this place and for a little while in Antarctica." He stopped for a moment, making sure he still had both men's attention. "Doctor Weir was a brilliant leader, she was passionate and she had the respect of everyone she worked with. And she cared about everyone she worked with as well. There isn't a doubt in my mind that Elizabeth would understand the reasons for destroying her once and for all." He could see Sheppard's head drop out of the corner of his eye. "But I think we owe it to her to try and help her."

* * *

John's head snapped up to face Daniel as soon as the words were spoken. He had been certain the archaeologist was going to side with O'Neill but it was a relief to have the man's support.

O'Neill appeared to have been struck dumb. He was staring at Jackson open mouthed. John wished he would say something.

Daniel did not flinch under the General's glare. Instead, he sighed loudly. "Jack?"

"Daniel?" His tone was curt.

"Oh, come on!" Daniel said in obvious exasperation. "You didn't have a problem going after Sha're and Ska'ara!"

John watched O'Neill stand up, seeing anger flare in him for the first time since he started this conversation. "That was different. They were Goa'uld! They could be saved!" He jabbed his finger at Daniel as he spoke.

Daniel's voice rose and he spoke with his hands flapping in front of him. "But we didn't know that at the start. And we went after them anyway!" He waited for O'Neill to come back, as did John. He had read the report on the abduction of Daniel's wife and brother-in-law by Apophis. It had never really occurred to him that Elizabeth's situation bore some interesting parallels to that. Daniel had seen it though. He thought about what Doctor Jackson had said earlier about working alongside her and could imagine that they got on well. Elizabeth always got on with people who debated passionately and intelligently.

When Jack still said nothing, Daniel continued, more calm than before. "Elizabeth Weir deserves no less than anyone else, Jack. What happened to leave no one behind?"

He turned to John and smiled slightly. John mouthed the words t_hank you._ Daniel nodded. As he waited patiently for O'Neill to find his voice – at the moment, John could only assume that he was weighing up the arguments for and against the mission – he realised there was one more point he could make. "There's another reason to revive her, General."

O'Neill looked from Jackson to him. "Really?" he said, tiredly.

"Yes," John ploughed on. "Elizabeth told us that in her… disembodied state she encountered lots of advanced races in the Pegasus Galaxy. That kind of intelligence could be useful – invaluable, even."

"Plus, she would be the perfect liaison to those races if we met them," added Daniel.

Both Sheppard and Jackson watched General O'Neill expectantly as he sat down and started tapping the table, a constant rhythm as he considered all the arguments. After what felt like a lifetime, the Head of Homeworld Security spoke. "Well, I don't see that I have much of a choice." He exhaled heavily. "Okay, I'll authorise the mission –"

"Yes, Sir," said John as he stood and saluted – though it was unnecessary, he couldn't help it. "Thank you, Sir."

"But…" O'Neill raised his finger, "I am only authorising it because of the tactical advantage that could be gained _and_ because advanced technology that could be used against us can't be left out there –" His hand did a flying motion, "- especially with the knowledge of Atlantis and Earth Weir has."

Sheppard nodded.

"The other Replicators have to be destroyed."

"Yes, Sir."

"And at the first sign of trouble from Elizabeth you have to be prepared to destroy her too." O'Neill locked eyes with Sheppard at this, as if searching for anything that would show his resolve wavering.

John could appreciate his caution. He really did not want to resort to that without trying everything to save her but if their attempts failed and she became dangerous he knew it was the right thing to do. "Understood, Sir."

"She'll be your responsibility, Colonel." At Sheppard's nod of acknowledgement, he turned to Jackson. "And yours."

John's nodding head froze as he looked from General O'Neill to Daniel and back again. "I don't understand."

Daniel looked at Jack. "You didn't tell him?" O'Neill shook his head. "You didn't tell him. Okay." He turned to John. "I'm coming with you."

Sheppard scanned the room, now recalling the sparse state he had been surprised by when he first came here searching for General O'Neill. "Is it a temporary thing or…?"

"No, no," Jackson said, beaming. "I'm joining the Expedition."

John wasn't sure how to respond to the news. Doctor Daniel Jackson would certainly be an asset, given his expertise in the Ancients and Ascension. But… well, there wasn't really a but – his presence could only be beneficial to the Expedition. He wondered how a certain Canadian Astrophysicist would react when he found out.

He quirked his eyebrows and smiled. "This could be fun." John turned and headed for the door. He had to start making serious plans now.

"John."

John turned back to General O'Neill, who was smiling. "Bring her home."

"Yes, Sir."


	8. Chapter 8

A/N: Sorry it has taken a little while. It seems to be an update every couple of weeks at the moment. Hope everyone is okay with that. This is a long one though. Please enjoy.

**Chapter 8**

It did not matter that none of what they were seeing was actually real. It did not matter that the bodies they inhabited were not real either. As Elizabeth and Janus stood in the Gate Room, she tried to recall a time when she felt more drained. She could not.

"Well," said Janus, quietly, breaking the silence. "They certainly subjected you to a terrible ordeal."

Elizabeth wanted to laugh. _A terrible ordeal_. One of life's – or non-life's – greatest understatements.

"Do you know why Oberoth tortured you in this way?"

When Elizabeth spoke, her voice was low, unsteady. "At the time I thought it was because he wanted to know Atlantis' destination."

"I take it that was not the case."

"No."

"But all those situations, all those nightmares. There had to be a better reason than just making you suffer."

"Oberoth was a vindictive, hateful bastard," said Elizabeth, coldly. "He took great pleasure in watching me suffer. He wanted to break me, to make me lose all hope. And he succeeded. But it was not his sole purpose."

"It wasn't?" Janus was shocked.

"The nanites in my body had been programmed by Rodney," explained Elizabeth. "He did it in such a way that they could not replicate or be manipulated, except by Rodney himself. Oberoth needed to probe my mind to find a way to counteract Rodney's measures."

"And then?"

The image of the Gate Room blurred and reformed. It became a laboratory, similar to any number of laboratories on Atlantis; brown walls, with glowing blue and white hues. A number of Replicators were gathered around an examination table. Elizabeth and Janus stepped up to one end of the table and saw her lying on it, still wearing the black uniform in which she had arrived. Oberoth stood off to the side, near the door. His expression did not change as he nodded. One of the Replicators to the right of the table acknowledged the nod and began to work. Within moments, he straightened up.

"And then, they turned me into one of them." The regret was still threatening to overwhelm her but she willed herself to stay strong. This was the moment her life truly ended. Doctor Elizabeth Weir did not argue, did not put up a fight and lay perfectly still as these monsters manipulated the nanites inside her, allowing them the freedom to replicate and transform her body. It angered her to know that she let them do it, did nothing to stop them. But after the torture she had given in. She knew she was alone. That no one would come for her, not even John Sheppard.

Janus seemed to know what she was thinking. "There was nothing you could have done to prevent this outcome. What Oberoth put you through was horrific; anyone would have lost hope after days or weeks of that."

Elizabeth turned to look at Janus. "It wasn't days or weeks." She shook her head. "It felt like years. But, in reality, it was seven hours."

"Seven hours?"

"Yes. It took seven hours for Oberoth to break me." She stared at the ground, too ashamed to face him.

"That's not true."

"It is."

"No!" said Janus, almost vehemently. Elizabeth gazed up at him in confusion. He breathed, and then extrapolated. "What I saw you go though was many years' worth of torture compressed into seven hours. Their ability to _manipulate_ your perception meant it felt like years. And it was. In some of those scenarios, you literally lived decades of your life. A lot of people would have broken before you did. And you still never told them the location of Atlantis."

"I didn't have to tell them," countered Elizabeth. "Once they turned me and I became part of the collective, they knew everything I knew, including where Atlantis was supposed to be going. Thankfully, John and Rodney were smart enough to realise they couldn't go there."

"Did it hurt?" asked Janus, as he watched the Replicator Elizabeth Weir sit up on the table. The difference was clear to see. The way she sat up straight, the neutral expression on her face, the lack of life in her eyes. This was no longer Elizabeth Weir.

"Like hell," answered the woman beside him. She looked to Janus and could see the trepidation as he watched the Replicator slide off the table and leave the room as part of the group.

"What was it like to be one of them? Did they treat you as an equal?" Janus was obviously curious now.

"They were wary of me to begin with. I would be stared at wherever I went. Everything I said was scrutinised but, in a way, I think I influenced them slightly."

"Why do you say that?"

"They didn't go after Atlantis, at least, not while I was there."

"So, they changed their minds?"

Elizabeth's head dipped to one side. "No," she confessed. "We reactivated the Wraith attack command in the Replicator nanite coding. Destroying Atlantis was still an objective but not a priority. There were problems, though."

"Really?"

"There was conflict within the collective. Some wanted to destroy Atlantis after they were done with the Wraith, others wanted to concentrate on other things like bettering themselves."

"And you?"

"I just wanted to be left alone." The laboratory faded and they found themselves on a balcony in a tall tower at the edge of the sprawling Asuran city. The Replicator Weir stood at the railing, staring at the ocean.

Elizabeth continued. "You see, they changed me and made me a machine but it was only a matter of weeks really when I realised that I would never truly be one of them. I still thought about my past life, longed to be back on Atlantis. But I worked hard to bury those feelings because I didn't want the others to know – somehow, I was able to do it. I just stayed away from the Asurans as much as possible. But…"

The door behind them opened and three Asurans came onto the balcony, two females and a male. One of the females, shorter than Elizabeth, was Caucasian with long straight dark hair and was recognisable as being on the council she had met with the first time she had come to Asuras with Sheppard's team. She stepped forward to address the newest addition to their number. "Doctor Weir?"

Replicator Weir turned around. "Can I help you?" Her voice was neutral, cold even.

"We seek your assistance in a matter of great importance to some of us," the woman stated.

"And what matter would that be?"

"Do you recall Niam?"

"Niam?" queried Janus.

The scene froze as the Replicator Weir was about to respond. Elizabeth faced Janus. "The first time I was on this planet we met an Asuran named Niam. He helped us escape and we took him with us. But they reprogrammed him and he tried to kill me. That was how I was infected with the nanites."

"I see."

Replicator Weir spoke. "I remember Niam, yes."

"Niam led a group of us who secretly engage in ways to reach the point of –"

"Ascension," Weir finished.

"Yes," said the female. "My name is Tana." She gestured to her companions and introduced them. The Asian female with short black hair was Delano and the tall blond male with a rather prominent hook nose was Ando. "We wish for you to help us in achieving Ascension."

"What would Oberoth have to say about this?" Elizabeth could see Weir's eyebrow arch upwards as she asked the question. It was one of the things that made her realise that she was still alive in there.

Ando spoke seriously. "If Oberoth were to know he would kill us or reprogramme us."

"Then why are you talking to me about it? What makes you think that I won't go and tell him what you just told me?"

"Because you are not like them. We can see that," answered Tana.

Weir immediately became apprehensive at this. She started to speak but Tana put her hand up as she interrupted. "Do not fear. The others have not seen this. You have hidden yourself well. Although, if Oberoth and the others were not so preoccupied with destroying the Wraith, I believe you would have been discovered."

Replicator Weir breathed a sigh of relief as she closed her eyes. She smiled slightly. "So, what would you like to know about Ascension?"

Tana also smiled. "Everything."

* * *

The area around them turned black. Then light flooded the space and they could see each other again.

Elizabeth sat down on the floor and waited as the Gate Room reformed around them. It had appeared in such a way as the Stargate was right behind her. She leaned back against the left side of the Gate and shut her eyes.

Janus sat cross-legged in front of her. "How are you?"

"Exhausted." Elizabeth felt her eyes well up and a tear run down her cheek. However, her lethargy meant that she did not wipe it away.

"So, what happened next?"

"I joined Niam's faction. None of them wanted the fighting to continue once the Wraith were defeated and they felt that targeting Atlantis would prevent their Ascension."

"Then what?"

Elizabeth smiled tiredly. "Can you give me a few minutes before we dive back in? It's pretty tiring."

"Of course," said Janus, nodding politely.

Elizabeth allowed her eyes to drift shut again. She could feel sleep overtaking her. She dreamed: of John, of Sedgewick, of Atlantis. In one dream, she was chasing her dog through the corridors, unable to catch her.

She awoke quickly but did not open her eyes. The images of Sedge running away from her disturbed her in ways she could not understand. It did not matter how fast she ran or how much she called out to her, she just couldn't get to her and the dog didn't seem to tire. Why did it hurt so much? It was just a dream.

"Are you all right?"

Elizabeth opened her eyes to see Janus sitting in the same position as when she fell asleep. He looked worried.

Elizabeth sat forward and placed a hand on his knee. "No." She paused and smiled. "But I think I could be." The dream was already fading away.

"Shall we continue?"

"Of course," said Elizabeth. "Where were we?"

"Niam's faction?"

She snapped her fingers. "Right." Janus stood and reached down to her. She took the proffered hand and he pulled her to her feet. As she stood the space changed again. This time it went black and they could see several things happening around them.

Elizabeth focused on the scene nearest them. In it, herself and twelve others sat in a circle, meditating. "I taught them how to meditate. I spoke to them about peace leading them to the path to Ascension and releasing your burden. They were eager to learn and I felt I had earned their trust."

She led Janus to the next scene. Replicator Weir was in an argument with Tana. "I was wrong to think that," Elizabeth said.

"You should have told me!" Weir said.

"It was not necessary for you to know." Tana spoke calmly.

"You used a clone of me!" Weir cried. "I had a right to know!"

"No, you did not," said Tana.

"But, why did you do it?"

"We wanted to learn about Ascension and we felt that having actual humans to observe would help us understand better."

"Well, it didn't work," declared Elizabeth. "All you managed to do was get my team and a large part of our number killed. A part of the group I didn't even know about."

"They were clones," pointed out Tana, "not your team. But something did come of it."

"What?"

"The clones made contact with Colonel Sheppard and his team. They were able to furnish them with a good deal of intelligence that will help them."

Weir's eyes narrowed. "What else?"

Tana sighed. "Your clone was told you were dead. I believe this information was passed onto Sheppard as well."

"Why?"

"Is it not obvious?" asked Tana. "Now they will stop looking for you. Now they will attack Oberoth with all their force and not be concerned for you."

Weir's anguish was clear on her face. Elizabeth remembered the moment with perfect clarity. It was as though time stood still. They would never come for her. She was alone. These… people were all she had left. And there was only one escape from the Replicator body. She had wanted to scream, shout, cry. She had wanted to snap Tana's neck. But she couldn't do any of those. She doubted this body could even produce tears and Tana would be able to stop her from causing her any harm. She had never been a fighter anyway.

Weir's face returned to a neutral expression. "What does this mean for the rest of us?"

"Oberoth is looking for us," Tana answered. "We are hidden from him for now but they will find us soon. We must prepare."

"Then there is something you need to do for me."

"What, Elizabeth?"

"I need to learn how to fight."

Tana nodded.

* * *

In the next part, they watched Weir training with different Asurans, but mostly Ando. They watched her fight hand-to-hand first. She was taken down several times but finally, Elizabeth felt pride as Weir crouched low, swept a leg out, kicking Ando's legs from under him and then with lightning speed, straddled his chest and punched him in the jaw several times until he shouted "Yield!"

Elizabeth also recalled learning how to use a variety of different weapons including Ancient and Wraith stunners, a sword and refining her training in the use of the P-90 and nine-millimetre handgun (John had been the one who had originally trained her though it was very basic, as neither of them had really wanted her to have to use guns).

The final lesson was how to destroy a Replicator. Weir stood in front of a Replicator - one that had been specifically created for this purpose.

"You must disrupt the bonds between the replicator blocks permanently," Ando instructed. "It is the only way to definitively disable one of our kind, not unlike the weapons your old team used against us."

Weir almost imperceptibly flinched at the mention of the "old team". She covered it by smirking slightly. "You got any ARGs lying around?"

Ando smiled. "There are some available but in a hand-to-hand situation you don't need one."

"What?"

"You have seen how we link with humans, correct?" She nodded. "We can also link to each other in this way."

Weir obviously remembered invading Oberoth's mind by pushing her hand into his head, as Elizabeth watched her swallow. "I'm aware of that."

Ando continued, not noticing anything. "When you force a connection you must probe until you find the command code for the nanites that are allowing the cohesion of the Replicator cells. Then it is a battle of wills."

"A battle of wills?"

"Yes, the strength of the opponents will determine who is successful. If the one who is probing is stronger, then they will be able to disrupt the nanite bonds and the Replicator will be destroyed. If the one being probed is stronger, then they will not allow their bonds to be broken and will eject the attacker from their mind."

"All right."

"Try it." Ando indicated to the new Replicator.

Weir turned to face the machine in front of her. It was merely a male body made of blocks, held together by nanites. There was no personality within the shell. Elizabeth, however, still remembered the nausea rising (despite the fact she was no longer human) as she observed Weir lift her right hand and force it into its forehead. Her face was a picture of concentration but as the moments passed, she visibly began to tire until she pulled her hand out and collapsed to the floor.

Janus started to step toward her but Elizabeth put a hand on his arm to stop him. He turned to her. "Were you able to do it?"

Elizabeth took a deep breath. "It took many attempts…"

Weir walked up to the Replicator. There were no signs of trepidation this time. She pushed her hand into its head again. Weir's face was not as before, she appeared to find what she was doing… amusing. It only took about ninety seconds for the machine to disintegrate into hundreds, thousands of tiny grey blocks.

Janus looked both pleased and horrified. "Impressive."

Elizabeth shook her head. "And all I needed to do was let go." She put her hand on her forehead. "Of everything that made me feel like I was still human."

"I'm sorry."

She let her head drop. "So am I."

* * *

Elizabeth lifted her head as the scenes faded out around them to be replaced by some sort of conference room. The brown and blue walls were indicative of the fact they were in the Asuran city but it was bigger than the one in the central control tower. Metal tables were pushed against the doors. Two other tables were opposite the doors but turned on their sides so the tops faced the door wall.

Elizabeth squared her shoulders and led Janus to the upturned tables. Weir and five of the faction were hiding behind them.

"Two weeks after the destruction of the faction's secret experiment involving my clone, they came for us."

They watched as the doors were breached by Oberoth and three Asurans who simply passed through the barriers in place. Weir and the others started firing their Ancient looking weapons but all they did was slow their enemies' advance down.

Weir fired and kept on firing, until she was face-to-face with a female Replicator with short auburn hair and a tanned face full of hatred. Weir dropped the weapon and punched the Replicator with her right hand. The Replicator's head snapped around for a moment, then she turned back and reciprocated. They punched and blocked and after several minutes of stalemate in which neither of them made contact with their blows, Weir took the initiative, spinning three hundred and sixty degrees and bringing her right leg up to connect with her opponent's jaw. The Replicator stumbled back. Weir ran at her, closing the gap between them in less than a second, grabbing her by the throat and slamming her to the floor. Climbing onto her whilst still gripping the front of her neck, she forcibly entered the Asuran's mind. It took but moments for there to be nothing beneath her but blocks.

Ando destroyed a second one, but Oberoth easily "killed" two of their own.

Elizabeth spoke to Janus. "But we had a plan."

Janus was unable to tear his eyes away. "Oh?"

Weir, Ando and their third Asuran colleague (a young looking black male named Seena who despatched Oberoth's other subordinate) surrounded Oberoth. Seena then ran to Oberoth and struck out. As he did this, Weir and Ando took the opportunity given to them and ran for the doors, throwing the desks aside with little effort and slamming through the nearest door. They hurtled down the corridor towards the open doorway ahead of them, smashing those who would try to stop them aside.

Elizabeth closed her eyes and the image around them blurred and reformed to become a pier, one that was located in one of the farthest areas of the city. Weir and Ando came barrelling through the doorway. Ando turned back and used the sensor to close the door, then pulled the casing off the panel, removed all the crystals and put them in his pocket.

A huge noise, not unlike a Tyrannosaurus Rex's roar – or several – was heard overhead. Elizabeth pointed upwards to show Janus. A ship was descending. It was massive and of Ancient design. A long, sleek grey vessel, the front housed the main bridge windows, the rear was wider to accommodate the hyperdrive and sublight engines. Janus gasped.

The ship landed, and a door at the front left side opened, steps forming to the ground. Weir and Ando ran up the stairs and inside.

"But… how?" stuttered Janus.

It was the first time in a long time Elizabeth genuinely smiled. "Everything happened very quickly. Oberoth was never aware of how many of us there were. A few of the group were working in the shipyards. When it became clear our time was short they set about prepping one of those ships for us to escape in. Only two of the builders were able to get away on it though. They picked us up on three different piers in various areas of the city. We went into hyperspace as soon as we got clear of the atmosphere."

As the ship lifted off, they watched. "How many of you escaped?" he shouted over the noise.

Elizabeth sighed. "Nine."

* * *

On the Bridge of the rebel Asuran vessel, _Ascension_ (Elizabeth named it), Weir sat in the captain's chair, looking out of the windows at the debris field. Her clothing had changed – drastically. She was wearing black leather boots, tight black trousers and a zipped up fitted black and red leather jacket. The rest of the crew stuck to the off-white suits.

"They've been completely wiped out," announced a female Replicator.

"Good," responded Weir. "We can finally get to work without looking over our shoulders. It's time to begin."

"How long after your escape before your people destroyed the Asuran homeworld?" asked Janus, seemingly mesmerised by the devastation beyond the ship.

"Only a week," said Elizabeth. "We came back after we received the intelligence report, but we made sure we arrived long after they were gone."

Activity on the Bridge continued around them. The _Ascension_ was sent into hyperspace.

"Where were you going?" queried Janus, studying Weir as she sat in the chair silently.

"To an uninhabited planet. It was known to the Asurans and the Ancients as Manis Proclarus."

"Yes," Janus remembered. "We had an outpost on the largest continent, underground. It was abandoned when the Wraith came."

"It was a planet that suited our needs. It had a moderate temperature, trees and grass. There was no sentient civilization and there was room enough to land the _Ascension_. It also had a Stargate if we needed a quick escape and an outpost with an Ancient chair, a working ZPM and a healthy amount of drones should we need to defend ourselves." Elizabeth watched as Weir got up and left the Bridge. "It was perfect."

Janus went to follow Weir. When Elizabeth did not, he took her hand and pulled her along.

The corridors were sterile and bright white. Weir stood out in stark contrast to the walls around her.

"I have one question," Janus said as they followed. "Why didn't you go back to Atlantis? You were free and they had put you in control."

Elizabeth did not know what to say. As she gathered herself, Weir went through a white door into her quarters. She sat on the bed in the sparse room and stared out the window. Streaks of blue and green of the hyperspace tunnel flew by but Weir did not appear to see them.

Elizabeth sat down next to her. "I wanted to go back, I truly did. But I wasn't one of them anymore. I was a danger to them, as were the others. I didn't want to put Colonel Sheppard in the position of having to kill me." A single tear started rolling down her cheek as she thought of the person she had missed – and still missed – the most. "It was better for them to continue believing I was dead. Plus -" she looked up at Janus, "- I owed these people for what they had done for me."

Janus folded his arms and looked down at both Elizabeth and Replicator Weir. "Oh, come on," he scoffed.

"Excuse me?" said Elizabeth, confused at his sudden change in attitude.

"You could have gone home!" exclaimed Janus. "I have seen the people you worked with. They would have accepted you back, Replicator or not! No, there's something else."

Elizabeth looked down at the plain white floor. She couldn't help the tears flowing freely now and didn't even want to. She sniffed to compose herself and looked at the Replicator by her side. There was a reason, but it was so personal that she didn't feel ready to say it aloud.

Janus waited, gazing at her. He wasn't going anywhere and he was not going to take her silence as a hint to leave it alone. Elizabeth," he said softly. "I can't help you if you are holding back. You need to release if you want to Ascend."

Elizabeth stood slowly and glared at him. "Release what? My burden? My shame?"

"Shame?"

She flopped back down on the bed, her legs suddenly weak, as she realised what she had revealed. She put her face in her hands and tried to regain control of herself. When she was sure she would not break down the moment she started speaking, she let her hands drop from her cheeks and once again stood to address Janus.

"Yes, shame," she confirmed. "I couldn't let him – them – see what I had become." She hoped he had missed the slip, but severely doubted it. "I was a monster."

Janus crouched down next to Weir. "Look at her." Elizabeth complied. "What do you see?"

"I see myself. A machine."

"Do you want to know what I see?" He paused, glancing up at Elizabeth before returning his scrutiny to her counterpart. "I see a woman in a terrible situation not of her own making who is lost and lonely. A woman so afraid of what she has become that she made the conscious decision to cut herself off from her family and seek escape by other means."

So moved by Janus' assessment, Elizabeth sat down again. But instead of thanking him or disagreeing she said something completely unrelated to his comments. "Even if I had wanted to, I didn't know where Atlantis was."

Janus smirked. "Excuses." At Elizabeth's questioning look, including the raised eyebrow, he qualified his response. "With your knowledge of Atlantis and the information you had at your disposal on this ship's database as well as that of the outpost you could have come up with a fairly accurate shortlist."

"I suppose," Elizabeth quietly admitted.

Janus straightened up from his crouching position and extended his hand to Elizabeth. "So what did you do once you reached Manis Proclarus?"

Their surroundings shifted once again and they found themselves in a clearing in a forest at night. Nine Replicators, including Elizabeth, Ando and Delano, sat around a fire, meditating.

"As you know," said Elizabeth, "our attempts to Ascend did not work."

Janus nodded. "So, what did you do?"

They shifted again. They were in a laboratory on the _Ascension_. Weir was lying on a table.

Elizabeth explained. "Koracen –" she pointed to a tall thin male with short brown hair "- developed a means to free a consciousness from a Replicator body. We would exist in subspace and be able to go wherever and do whatever we wanted. He called it Technological Ascension."

They watched as what looked like a bolt of lightning struck Replicator Weir and she disintegrated. Nothing more than tiny blocks remained. Elizabeth walked over to the table and reached out to touch the pile of tiny puzzle pieces that had been her body.

_This is all I was,_ she thought. _And I let them take it away from me._

* * *

Elizabeth cycled quickly through the next period of her existence. Technological Ascension did not quite meet expectations. She travelled the galaxy. But she could only interact with machines and the pain of her condition was unbearable.

When no way of alleviating their situation could be found she agreed to return to Atlantis and convince the Expedition to help them.

She showed Janus all that happened on Atlantis right up to her final glance to John Sheppard before she stepped through the Stargate.

Janus breathed heavily. "It was your idea to trick the others."

"It was," said Elizabeth. "Although I did not know where exactly we would be sent. I didn't want to in case one of the others was able to read it in me."

The Gate Room dimmed and the event horizon and people disappeared.

"I understand," Janus declared.

"Understand what?" said Elizabeth as she stared at the Stargate.

"Why you couldn't Ascend."

Elizabeth turned to him. "Go on."

"First of all, Ascension is a higher state of being. You cannot use it as a way to escape your current existence. You _release_ your burden, you cannot run away from it."

Elizabeth nodded. "I see what you're saying. I suppose you are right. I did see Ascension as a way of getting out."

"You still feel ashamed?"

She nodded again. "It makes me so angry that these things happened to me and I didn't stop them." She ran her hands through her hair and pulled at it as she reached the ends. Her frustration at herself grew with the volume of her voice. "I shouldn't have let any of it happen. I should have told Rodney to shut off the nanites when I woke up. I should have fought Oberoth harder, done something to make him kill me rather than change me. I should have found a way to escape from them as soon as I realised that I was still me, despite the changes… I should have…I should have…" She slowly sank down to the floor, sitting with her feet on the steps.

Janus sat next to her. "There's another reason, isn't there?"

Elizabeth's head, still bowed down, turned to Janus. "There is?"

"I told you before that to Ascend you must be able to release both your past and your hopes for the future."

"Yes?"

"You had hopes for something in particular, didn't you?" When Elizabeth didn't reply, he carried on. "John Sheppard."

Elizabeth was not entirely surprised that Janus had figured out her feelings for John. She still considered lying, denying it. It was a force of habit. She had never told anyone that she loved John and had deliberately buried her feelings.

However, despite the way she denied it and continued with her daily life, her spare moments (as few as they were) and dreams would often give her glimpses of what a life with him could be like. Her time in space allowed her to elaborate on these possibilities and she was never able to see how a relationship with him could go wrong, even though she consciously spent time telling herself why it could never have worked between them when she was "normal".

Janus would be the first person she ever confided in if she chose to take the course he presented. Would it help her Ascend? It was highly unlikely. How could she stop loving him? Janus had done so much for her already, though. She found she could not lie to him.

Decision made, she got up and turned to the stairs leading up to the balcony. As she walked towards the area, Janus trailing behind, the image reset. They saw herself appear and stand in front of the window as in the first scene she showed him. Once again, the sky turned red and the glass started to shatter as Elizabeth put her arms up to protect herself. The image froze.

Elizabeth turned to Janus. "This was my last conscious moment as a living human. As the beam hit I knew I was going to die, was absolutely certain of it. And this is what I thought of as I died."

She looked down to the platform in front of the Stargate. Four men beamed into the space. One of them was John Sheppard.

Elizabeth and Janus walked back as John gave instructions and turned to see Elizabeth walk down the steps from the Control Room towards him. They gazed at each other for a moment and she reached out and hugged him. He was obviously surprised but soon moved to return the hug. As she pulled back, she looked into his eyes. John's head moved down and he kissed her. She kissed him back, her fingers moving through his hair.

The scene froze. Elizabeth sighed sadly. "It was only at that moment of dying that I realised that I wished he knew how I felt. It always seemed easier to keep it to myself before, for the sake of Atlantis." As she walked around the couple in her fantasy, she spoke her thoughts aloud. "John Sheppard meant everything to me. I loved him more than I thought possible. But I always believed that he could never feel the same for me as I did for him. He was far more suited to someone like Teyla, a strong woman who fought like he did. I kept my feelings to myself and, apart from one hug and a kiss when we were possessed by aliens, my feelings and fantasies remained in my head."

"But…?"

But looking back…" Elizabeth paused. "The way we would look into each other's eyes and each know what the other was thinking… the way he would watch me when he thought I was too busy to notice… he went out of his way to find me a birthday present in the Pegasus Galaxy. He risked his life when he broke the quarantine to be with me when I was first infected by the nanites." She shook her head. "I don't know, maybe I was wrong." She finally stopped beside Janus and the image returned to the empty Gate Room. "It doesn't matter now."

"You can't ascend while you continue to hold onto him," Janus said gently.

"I can't stop loving him, Janus. I already tried, believe me."

"You don't have to stop," he responded. "You only need to accept that you love him but it will never be. Be glad that you were able to feel such wonderful emotions, that you met him."

He took both her hands in his own. "The others always speak in riddles at this point but I think it is unnecessary. Terrible things happened but you are still here. Your strength is unsurpassable. Accept your, past, embrace it, even. All those events led to this moment."

Elizabeth closed her eyes. Could she do what Janus said? Viewing it all the way they had was difficult but she was able to do it. She only ever did what she believed to be right at the time, although sometimes they turned out to be wrong. She did rebel against those who made her like this, despite the dangers. And she never completely lost herself, even after everything they did to her, after all she had been through.

She would always love John. But would it have been better for her to never have met him so that she would never have had to feel the pain of losing him? _No._ She was a better person for having loved someone so completely.

Something was happening. She opened her eyes to see Janus bathed in light. She then looked down and saw that the light was around her hands and arms as well. Surprised, she looked at Janus who was grinning at her. The light around them shone brightly, giving them an ethereal glow.

"It's time." Janus let go of one of her hands and waved towards the Stargate. The event horizon appeared before them – without the onrush of the pool first.

Hand-in-hand, they walked towards the 'Gate. As they reached the threshold, they paused. Elizabeth turned back to survey her home for one last time, her eyes stopping when they reached the balcony overlooking the Gate Room.

Leaning on the railing, looking down at her, was John Sheppard. He smiled at her.

Elizabeth smiled back and mouthed one word, _Goodbye._

She turned back and stepped through the Stargate. A new journey was waiting for her on the other side.


	9. Chapter 9

**A/N:** This is a note of the most profuse apologies for how long it has taken for me to post this chapter. It has been a tough time. Things like severe illness of both myself and my child, school holidays, work and some life changing news all contributed. Perhaps I was too eager in my initial goal setting as well, stating a chapter a week. It seems with my life that will not be possible. I can at least say that Chapter 10 is already written and checked so should be up very soon. After that, it will most likely be every three weeks. But I don't plan to stop. There is still too much going on in my head for that to happen.

Anyway, I hope everyone enjoys Chapter 9.

Note: Stargate: Atlantis is NOT mine.

**Chapter 9**

Richard Woolsey called all the senior staff into the conference room. John Sheppard and his team sat around the mahogany table, along with Doctors Keller and Beckett, Lieutenant Colonel Lorne and Woolsey himself. The walls were also lined with all the various department heads, as well as Colonels Caldwell, Carter and Ellis, commanders of the three present Earth ships.

Woolsey stood from his chair at the head of the table. "Thank you for coming. I felt it was important that you all know as soon as possible." He paused, though John was fairly certain it was for dramatic effect. "General O'Neill has informed me that the International Oversight Advisory, the military and Homeworld Security have agreed that Atlantis should return to the Pegasus Galaxy as soon as all repairs have been completed."

The revelation was greeted by a number of somewhat unprofessional whoops and cheers. John – who had known since the day before – kept his focus on Ronon and, particularly, Teyla. He hid a smile as Ronon slammed the table with his fist, a huge grin on his face. Teyla was somewhere between laughing and crying, joyful tears rolling down her cheeks as she listened to something Keller was whispering to her. John was happy for her; no one deserved this more than she.

Woolsey raised his hands in a silent plea for calm. "Now, there are still a large number of debriefings to be completed and everyone will be given a few days' leave after their debriefing." At Rodney's raised hand, "Yes, Doctor, you are clear to start your leave as soon as this meeting is over."

He cleared his throat and continued. "However, this is important. I understand that whilst everyone agrees that Atlantis belongs in Pegasus, there may well be some who wish to remain here on Earth. Therefore, I want all department heads to speak to your teams and ask if there is anyone who would like to stay. I want everyone's answer in seven days' time." There was quiet murmuring around the room.

Woolsey sat down. "Thank you. Dismissed." He started writing on his notepad as everyone started filing out. "Colonel, if you and your team can stay."

John hadn't even started to get up. The others had, however. Ronon, Teyla and McKay sat back down. Rodney was muttering under his breath. They waited patiently.

Sheppard did not know that Woolsey was going to give everyone the choice of whether to remain with Expedition. He was pleased when he heard him say it. These people had been through so much, some since the beginning. Every one of them deserved the chance to start afresh or go back to their old lives. It wasn't an option he planned to take up of course; his place was on Atlantis – at least for the time being. Woolsey looked up. "Colonel, I understand General O'Neill told you the news yesterday."

The members of his team all turned to him.

"You already knew?" questioned Teyla.

"Why didn't you say something?" demanded Rodney.

John noted Ronon's stern glare and shrugged. "He told me before it was official. I couldn't say anything."

Rodney sat back. "Military!" he snorted. Ronon and Teyla also accepted the explanation.

"What else did you discuss?" Woolsey asked.

It felt as though all the air had been sucked from the room. What was Woolsey asking? What did he know? He couldn't believe that General O'Neill would have told him about the mission. He had expressly ordered Sheppard to keep quiet, to not tell _anyone_ until Atlantis was home. Less chance of the IOA finding out and putting a stop to it. But if Woolsey knew, then the IOA did as well. Part of Sheppard wanted to panic. However, the military man won out and he remained calm. It was not a certainty that Woolsey knew anything. And he wasn't going to incriminate himself. So he answered the question in another way – they did, in fact, discuss more than the mission. "We may have talked about a new Expedition member." John stated evenly.

Woolsey's eyes lit up and he nodded. "And what is your opinion on the new addition?" Woolsey's eyes moved to the side slightly and John could see he was glancing at McKay.

_That's what this is about?_ John thought, incredulously. He felt his heart rate slow down again and he exhaled heavily in relief, though it would look like a sigh at Woolsey's question. It was all right. Woolsey didn't know about Elizabeth.

He almost chuckled at the situation. It was ridiculous. Richard Woolsey, leader of the greatest endeavour of humankind, was afraid of revealing to a subordinate – a grown man – a particular person was joining the Expedition and wanted John's help to break the news.

However, given Rodney McKay's tempestuous nature and immature attitude, not to mention his massive-yet-sensitive ego, John could understand Woolsey's apprehension. Daniel Jackson's knowledge of the Ancients possibly surpassed McKay's own – certainly in relation to the language and culture. His impending arrival would make the scientist very unhappy and when he was unhappy, John and everyone else heard about it – _a lot. _He did not like being seen as anything less than the most important person on Atlantis. To him, Jackson would not be a colleague, but a rival. Perhaps the fact that Rodney was literally about to leave the base meant now was the best time to tell him – at least he would have a few days' peace before the diatribes began.

John finally answered Woolsey's question, thereby agreeing to assist in the matter. Truth be told, he and Teyla were perhaps the only ones who could keep him calm. Well, besides Carson who had already left the room, and Elizabeth. "I think he'll fit in great."

Rodney was looking at both of them with a look of impatience on his face. "Would you stop playing 'Mystery Guest' already? Who are you talking about?" he demanded.

Oh, John was enjoying this. A few days ago, this would have only given him a fraction of the pleasure he was feeling now. Funny how quickly things changed. Nothing had changed for him for a long time – not within. It felt good.

Woolsey leaned forward and spoke gently. "Daniel Jackson."

Rodney looked around the table. John could see everyone holding their breath as they waited for him to explode.

"Oh."

John started talking, trying to soothe him. "Rodney, I know that you had a problem with him the last time he was here but he is an expert on the…" He trailed off. McKay was sitting beside him, perfectly calm. He wasn't pacing the room, swinging his arms or ranting. "Wait a minute. Are you okay, Rodney?"

"I'm fine," he said pleasantly.

John exchanged looks with Ronon, Teyla and Woolsey, all of whom looked as bewildered as he felt. "So, you're okay with this?" he asked warily.

Rodney shrugged. "Why wouldn't I be?" he said cheerfully. "Doctor Jackson is an expert on the Ancients and their language and we could really do with one of those. Plus, after the whole getting-kidnapped-by-renegade-Asgard-nearly-dying thing, I think we'll get on fine."

Sheppard wanted to say something, anything. Nothing sprang to mind. The man he paradoxically considered to be the biggest pain in his backside as well as one of his best friends was behaving incredibly rationally and it was confusing the hell out of him. He briefly entertained the idea that Rodney was being like this on purpose to annoy him but dismissed it. His ego would never allow room for that. God, he was actually dumbfounded. "Uh… great."

McKay pointed at the conference room doors. "Can I…?"

Woolsey's head dipped. "Of course."

McKay got up, grinning and rubbing his hands together. "Well… see you guys in five days." He waved and all but ran out of the room.

They all watched him leave.

Woolsey broke the silence. "That was…"

"Wow," was all Sheppard could find in his vocabulary to describe what had just happened.

Teyla followed. "Good?"

Ronon completed the thought in his own succinct way. "Weird."

John Sheppard strode purposefully down the corridors of his home. It was a hive of activity with people working to make the final preparations for Atlantis' departure from Earth.

Now, six weeks since the authorisation of his mission (which John had unofficially dubbed Operation Sedgewick – only a few would know that was the name of Elizabeth's dog), John was still getting used to feeling happy. It had been so long since he had felt an honest-to-God positive emotion. But he had done everything he could to keep himself in check. He didn't want anyone realising he was hiding something. However, everyone now and then he caught himself out – singing in the shower, laughing at some curt remark Rodney had made, having fun when Ronon was beating the crap out of him. Yesterday, he had drawn strange looks in McKay's laboratory whilst looking at a mysterious Ancient device. It was at that moment he noticed he was whistling. Whistling! He had quietly apologised and exited in a hurry.

Tomorrow was the big day. Rodney had left for his break incredibly excited to see his family. Five days later, he returned having seen his sister Jeannie and her family, as well as meeting his girlfriend's father for the first time (which according to Rodney was more terrifying than confronting a Wraith Queen. Jennifer seemed quite happy when he asked, saying it could have been worse). He was grumpy as ever and ready to lead the repair effort. In the weeks that followed he and his teams had practically worked around the clock. Fixing the star drive had been difficult, until McKay remembered the Ancient deep sea diving suits they had appropriated from the underwater drilling platform on Lantea three years before.

Of course, keeping San Francisco Bay off limits for this long was becoming a real headache for everyone, especially the President. Boats, planes and people were out of bounds. Unsurprisingly, attempts were made to breach the perimeter, but so far, so good. The military had kept the gawkers out.

John arrived at his destination and used the sensor panel to signal his presence. The doors were opened from within by Doctor Daniel Jackson.

"Hi, John," he said as he rushed back into his new quarters.

"Doctor," replied John, following him in. The room was chockfull of cardboard boxes and grey crates. The newest member of the Expedition obviously hadn't had time to unpack yet, but then he had just arrived.

"Please, it's Daniel," Jackson said. He moved a box from a chair by the desk and put it on the single bed. He gestured to John to take the chair whilst he sat on the bed by the box.

John picked up the proffered chair and moved it to sit opposite Daniel. "So," he started, "like your new digs?"

Daniel looked around. "Oh, they're nice." He pointed to a pile of crates that all but obscured the window. "Certainly got a great view."

"Most rooms here do," agreed John, smiling proudly. His city was beautiful, no one could deny that.

Daniel leaned forward and spoke quietly. "You told anyone yet?"

John felt compelled to keep his voice at a similar level. "Told anyone what?"

"About the mission."

John shook his head. "General O'Neill ordered me not to say anything until we were back on New Lantea."

Daniel nodded. "Yeah, Jack said he was worried you might mention it to your team."

John was surprised that he felt a little injured by that. He was career military, keeping secrets was part of the job. However, if he was completely honest with himself, it had been difficult keeping his mood under control. He was sure that Teyla would have noticed, if not Rodney and Ronon. It was part of the reason he was keeping his distance from her now. It had been so hard when he arrived back on Atlantis six weeks ago to not run straight to Teyla's quarters and tell her everything about Operation Sedgewick. Originally, he had been avoiding her because he didn't want to talk about Elizabeth. Now he was avoiding her because he was desperate to. "General O'Neill does know that I work in a top secret programme, right?" he said, sarcastically.

Daniel responded with a small smile. "But, they're your team. You're close to them." At this, John nodded, knowing that Daniel understood the dynamics of working as part of a team – a team that travelled to different planets and ran into all sorts of dangers. That sort of life bonded you in ways no one could imagine unless they had been through it themselves. "Anyway," Daniel continued, "they're going to be part of the rescue mission, aren't they?"

"They are," said John, "if they want to be."

"I don't understand."

"This is my mission and it might be dangerous." He paused, not wanting to say it but he couldn't ignore the possibility. "She might be dangerous. I'm not going to order anyone to take that risk." He felt a surge of pride as he thought of the people he was going to _ask._ "But, I think they'll want to help Eliz – Doctor Weir." He knew he shouldn't have, but he let his eyes drop to the floor. "They're good people."

John was aware it was a risky strategy, asking the people he had in mind to volunteer. The fact was he needed them, couldn't do it without them. Particularly one annoying, arrogant Replicator expert. McKay was the one who could revive Elizabeth and help build her new body. Ronon, Teyla and Lorne would assist in destroying the other Replicators and be there in case things got… messy. He was almost one hundred per cent sure that they would all say yes. But if McKay didn't co-operate he didn't really have a fall back option. The mere thought, however unlikely, scared him more than he would admit. McKay, unfortunately, was the key.

"Have you figured it all out yet?" asked Daniel.

John grinned. Having Daniel Jackson on Atlantis was going to be a good thing. He would never forget that the man before him had been instrumental in getting Operation Sedgewick authorised and now he was here. Someone who knew John's intentions and was able to discuss the finer points with him until a full-blown plan was formed. This would make it easier to carry the secret – he was not alone.

"For the most part," he said. "I do have one problem though."

"What's that?"

"Woolsey."

"Woolsey?"

"I don't really want to take a jumper and some ARGs –"

"ARGs?"

"Anti-Replicator Guns."

"Ah."

John continued. "And go through the 'Gate without Woolsey knowing why."

"Would it be possible to do that?"

John's head bobbed up and down as he spoke. "Oh, yeah, the Control Room is skeleton-crewed during the night. It would be easy to go then."

"So… what's stopping you doing that?"

"Firstly, Woolsey probably wouldn't be too happy to let us back through, especially once he finds out we've got… an extra passenger." He sighed. "Plus, I kind of like the guy. I don't really wanna deceive him."

"You don't?" Daniel sounded surprised by that.

"No." John couldn't really blame Daniel for his reaction. It surprised him too. A couple of years ago he had wanted to punch the balding man for his apparent disrespect for Elizabeth and her position as leader of Atlantis. When he heard that this person was going to be taking charge he had been horrified, had even considered for a moment resigning his post. But time had shown him that Richard Woolsey was a capable, if somewhat cautious leader. He respected him. But nothing could get in the way of this mission and if he had to lie to Woolsey he would. He wished he could think of another way.

"There is another way," said Daniel.

John did a double take. Did Jackson read his mind? "What's that?"

"Tell Woolsey the truth."

John looked at him to confirm he was serious. When he could see only a straight face, he couldn't help but scoff. "I don't think so."

"Why not?"

"He'll never allow it. He'll probably tell the IOA."

"Look," Daniel began, his voice rational. "This is a military mission that's already been authorised by the Head of Homeworld Security. The IOA have no control over military matters, so Woolsey can't stop you. It's more a matter of telling him so you can get what you need to complete the mission."

"So why tell him at all?" asked John. While lying to Woolsey didn't sit well with him, pulling the whole "classified information" thing seemed easier. He could tell him what he required but not the reasons. Though was there the chance that that was a lie of omission? Still it was an option.

"Well, I think he needs to know."

"Why?" Although he wasn't sure he wanted to go down that road, he still wanted to know Daniel's rationale for telling Woolsey everything. He was playing Devil's Advocate, he supposed, asking the questions so he could hear all the arguments before making as fully informed a decision as possible – working with her for three years had rubbed off on him.

"Well, the fact is he is in charge and whilst rescuing Doctor Weir is a military operation, giving her a human body is a scientific one and – "

John realised what Daniel was saying. "The scientists are employed by the IOA."

"Not to mention the fact that you're going to be using a part of the city he runs to house her and create that body."

Daniel was right, completely and utterly right. He had to tell Woosley before Operation Sedgewick was put into action.

He put his face in his hands and groaned. Dammit, why did he have to be right? Maybe this was what General O'Neill meant when he told him Daniel Jackson could be a "moralistic, self-righteous pain in the ass."

He had only a pessimistic idea of how the conversation with Woolsey would go – and it was not a conversation he wanted to have. Maybe it would go better if he was able to tell him he had a plan and volunteers. Which meant – "Okay, I'll tell him, but, only after I've talked to the others."

Daniel nodded his agreement. "Sure. You know, Woolsey may surprise you."

"You think?" John couldn't keep the curt edge out of his voice.

"Maybe."

John stood. All this debating was making him hungry. He checked his watch and noted it was lunchtime.

Daniel started opening the box on his bed. Sheppard knew he was a good person before all this but it wasn't until the last month or so that he realised how true that was. He was also knowledgeable, had a strong sense of right and wrong and wasn't afraid to stand up for what he believed in. Not unlike someone else he knew. He could see why Elizabeth held him in such high regard. He recalled her saying once that she wished Daniel had been able to join the Expedition, both because of his area of expertise and also to have him as non-military support when she butted heads with the SGC and the IOA. At the time John had been a little put out, perhaps irrationally, but he wondered if she had felt he wasn't giving her enough support for her to start requiring it from elsewhere.

Now he understood. Daniel would have agreed with her assessment of the plan to destroy the Replicator shipyards, stood at her side as she fought it, unlike John himself. He had turned away from her, even partaking in the mission to which she had strongly objected. This was what he had pinpointed as the moment where things started to go wrong. It was followed by the Replicators' reprisal attack on Atlantis, leaving Lantea, Elizabeth being severely injured and eventually leading to her loss. Perhaps if Daniel had been here he would have supported her in the way John should have.

John mentally shook himself out of those thoughts. He had spent a very long time brooding over those events, wondering if he had done things differently, would she have been hurt. He had let her down. It wasn't the first time and it definitely wasn't the last. But he had committed to memory the expression on her face as she wished him luck for the mission. It was not difficult to see the feelings of betrayal and disappointment directed at him. Of all the times he had let her down (and there were far too many of them), he suspected that was the one that hurt her the most. It still tore at his soul when remembered it.

But it didn't matter now. He was going to get her back. And he was going to spend the rest of his life making it up to her – if she allowed him to.

As he watched the other man remove some books from the box he made a decision. Elizabeth considered Daniel Jackson a friend. He was going to do so as well. "Do you want to get something to eat?"

Daniel looked around the room and dropped the books back in the box as he got up, smiling. "Sure, why not?"

Teyla Emmagan slowly chewed her food as she watched Rodney McKay shovel his down, as he described how much he still had to do in order to make sure that Atlantis was fully prepared to leave Earth tomorrow. She had learned long ago how to tune out the verbal tornado that was Doctor McKay without him realising, whilst also being able to pick out the things she did need to know.

This time, however, she was not paying enough attention to pick out anything. Her stomach was aflutter as she contemplated her reunion with her partner and son. She missed Kanaan and Torren greatly but it had been the right decision for them to remain in Pegasus, going to New Athos to be with their people. The mission had been far too dangerous and she did not regret it. But her dreams were filled with her family. Torren would have changed so much in the time that had passed. She felt a small pang of fear as she wondered if Torren would recognise his mother. She pushed the fear down and turned her attention to her eating companions to divert her mind.

Ronon was sitting next to her, having just returned with his second serving of… everything. He never listened to what McKay was saying either. Ronon had been a good friend to her since they had met five years ago but especially in the last seven weeks. In spite of his developing relationship with Amelia Banks he had been there to provide her with whatever it was she required, whether it was a shoulder to cry on, a sparring session or, on a few occasions, someone to talk to – not that he had done a lot of talking but the listening was helpful anyway.

Rodney had tried to be supportive. At first, he had tried to talk to her about how she felt but it was awkward. After the second attempt he fell back on what he knew best – a progress report. After that, he would visit her wherever she was in the evening to give her daily updates on how the repairs to Atlantis were going and the timeframe for completion. And with each report, in which the Doctor's estimated time of completion shrunk, she felt her anticipation grow. Until yesterday, when he had come to the gym and confirmed that Atlantis would be departing on schedule. Amazingly, Rodney had given her more comfort than anyone.

Teyla had been overjoyed at the time. But since then the nerves had grown and her normally calm mind was creating all sorts of worries and concerns. She was doing her best to keep her thoughts off them but it was not easy.

Teyla looked up to see John Sheppard and Doctor Jackson moving towards their table on the balcony off the Mess Hall.

There was something different about John. Since his return from his leave he was … better. Of course he had barely spoken to Teyla unless others were around – she had expected as much given the way their conversation had gone at the party all that time ago. But it was obvious that something had changed for him. Gone was the slight slouch she had become accustomed to seeing, he walked taller now and his tone of voice had taken on a more cheerful lilt. The differences were subtle and she doubted Rodney or Ronon would have seen them. But she did. These were remnants of the old John Sheppard and Teyla was glad to see it. Her curiosity as to what had brought about this change was piqued but she dared not ask. His misdirected anger after his revelation to her led to the decision to heed his wishes and not discuss Elizabeth – or anything else personal to him. Not that he had given her the opportunity to do so. But, this was only temporary. One day they would talk about her. They would also talk about the way he had been avoiding her at a time when she really needed his friendship. She had to acknowledge a certain amount of disappointment in him. She had hoped he would be able to put what happened between them aside and give her some level of comfort or distraction, as Rodney, Ronon and many others had. It was a surprise to her as in the past this had not been the case. As part of the team, they were close, very close, and looked after each other.

Both men sat down.

"Hi, guys," said Doctor Jackson happily.

Ronon grunted a greeting as he continued eating. Rodney picked up his tablet from beside his empty plate and muttered "hello" as he left the table.

John and Doctor Jackson stared after the departing scientist for a moment, then looked at each other. John shrugged and picked up his sandwich. Jackson looked as though he wanted to say something but did not.

"Hello, Doctor Jackson," greeted Teyla, hoping that if she showed the man some courtesy it would make up for her friends' less than polite behaviour. "Welcome to Atlantis."

"Thanks, Teyla," said Doctor Jackson, a relieved expression on his face. "It's great to be here. It's Daniel by the way."

Teyla bowed her head slightly. "Very well…Daniel."

"Is McKay pissed about something?" asked John, as he took a sip from a bottle of water.

Ronon shrugged. "Dunno, he seemed fine before you got here." He looked pointedly at Sheppard.

Teyla shot Ronon a glare. She had previously overheard Rodney and Ronon discussing Sheppard's evasion of Teyla and were quite angry about it, though neither had confronted him. Rodney had chosen to express his dissatisfaction in more – what was it Kate Heightmeyer called it? – passive-aggressive ways: not staying at the table when John joined them for a meal, constant sniping remarks. John, however, barely noticed the difference. Ronon's display of frustration was more aggressive and much less passive. He simply gave Sheppard far harder beatings during their sparring sessions and said very little to him. Again, John was unaware of the shift in behaviour. No, his thoughts were elsewhere.

Teyla chose not to explain to them the true circumstances surrounding the tension between herself and John. It would have been a violation of the trust he had placed in her when he had told her of his feelings for Elizabeth. Unfortunately, this meant that she had to allow them to believe that he was staying away from her because he was uncomfortable with her situation. Yet, she was quite certain he would prefer they thought that than she tell them the truth.

She watched John as he laughed and joked with Doctor Jackson. It had been a long time since she had seen him so relaxed. He looked over and smiled. And there it was. A sparkle in his hazel eyes. It was the first time she had seen that for over two years. Something had definitely changed. Teyla wondered if it could possibly be related to Elizabeth but she could not figure out how. She dispensed with attempting to guess the reason. If and when John was ready to talk about it, he would.

And, as his friend, Teyla would be there to listen.

Daniel walked slowly back to his quarters, making mental notes of the route he was taking from the transporter. It was going to take a good while for him to learn how to get around Atlantis. He could envisage himself getting lost. A lot.

He was in a good mood. For so long, he had wanted to be here in this city, to be one of those unlocking the secrets it held. He had honestly believed Jack was playing a trick on him when he asked him if he wanted to join the Expedition. He had held his nerve as he narrowed his eyes and calmly answered that he would and then waited for Jack to deliver the punchline. Instead, his best friend had smiled at him and shook his hand, saying one word, "Done!" Despite the grin, Daniel could see that his eyes were tinged with sadness and he could understand why. He was going to miss him too. He was going to miss everyone. But with Sam rarely on Earth these last couple of years and now taking command of the _General Hammond_, Teal'c spending more and more time with the Jaffa and Jack now based in Washington D.C, the only people he saw regularly whom he considered as close friends were Cameron Mitchell and Vala. Oh, and General Landry and Doctor Lam. But he would miss them all – even Sergeant Harriman.

This, though, was a once-in-a-lifetime opportunity. How could he pass it up? The excitement within him was threatening to cause his heart to beat so fast until it burst out of his chest. He wasn't sure what excited him the most. Was it finding technology and discovering its purpose? Was it learning more about the Ancients' history? Was it meeting new races and cultures in another galaxy?

No, frankly, what he was looking forward to most right now was the journey. He was going to be here when the city lifted off from Earth and began the long trip back to the Pegasus Galaxy. He had spent twenty minutes of lunch asking Sheppard, Ronon and Teyla what it was like. Ronon said it was fine. Teyla told him that being in the City of the Ancestors as it travelled through space was awe-inspiring. Sheppard had not answered the question, instead finishing his sandwich and excusing himself from the table.

_Where am I?_ Daniel turned back the way he came.

John Sheppard had been very welcoming. Daniel suspected it was partially because he was the only other person in Atlantis who knew. He was grateful anyway.

He had spent the last month replaying the conversation in which Jack authorised the mission in his head. The more he thought about it, the more obvious it seemed to him that John had omitted one thing in his reasons for saving Doctor Weir. He had called her a miracle for God's sake! He was in love with her, of that he had no doubt.

He had considered asking John about it, but years of experience taught him that when it came to military officers and their feelings for others, it was better to leave it alone. He had watched two of his best friends wrestle with the "unspoken love quandary" for years. But they always put the Stargate Programme first and so it was not resolved. Jack O'Neill always went into denial if Daniel even approached the general area of the topic, while Samantha Carter just went quiet.

It took Jack's relocation to D.C. and another eight months before they decided to take the chance. It was a long distance relationship but they were both happy. And Daniel was happy for them, as was Teal'c, who had even smiled when they announced the news – a little anyway. Daniel liked to think that General George Hammond and Doctor Janet Frasier would have been pleased for them too.

He stopped at a dead end. "This isn't right," he mumbled and retraced his steps.

However, though Daniel was aware of Jack and Sam's feelings for each other, in this case he could only say that John Sheppard loved Elizabeth. He had no idea if she had reciprocated. It was strange. Before her involvement in the Stargate Programme Doctor Elizabeth Weir was a world-renowned diplomat and negotiator and part of her philosophy was that the way to stop the military of any country having too much power was to stop the need for having a military in the first the place. Seeing her working with the military for as long as she did was a surprise. Could he imagine her falling in love with a man in the military? He knew from discussions with her that she was fond of John and that she deeply respected him. And having worked with the military himself for many years now, he knew that Colonel John Sheppard was not a typical officer. So, yes, ironically, he could see the possibility. But he knew Elizabeth well enough to know that if she did feel the same, she would not have told him, choosing instead to put Atlantis before herself and probably expecting that if she did acknowledge those feelings publically, the IOA would have removed her as leader. They probably would have.

It was all like an Ancient Greek tragedy when one put it together. Two people in love but unable to be together due to their roles in the city and then one being taken away from the other, neither of them ever knowing the truth of each other's feelings.

Finally arriving at his quarters, Daniel entered and went immediately to the bathroom to wash his face.

Upon exiting, he jumped back in shock, holding back a yelp of pain as his right shoulder hit the doorframe behind him. "What the hell?"

A woman was sitting on his bed. A very familiar, incredibly annoying woman. Her long black, wavy hair was loose around her shoulders. She wore a tight green low cut knee length dress and her bare legs were crossed. Her facial expression was one of complete innocence.

Straightening up in an effort to retain a small measure of dignity after the initial horror and stumble, he spoke sternly. "How did you get in here?"

Vala Mal Doran smiled seductively. "I have my ways."

Daniel changed tack, still livid that she had come into his room without permission – yet again. "What do you want?"

Vala got up slowly. "I came to say goodbye." She walked towards him, her hips swaying, nicely accentuated by her attire.

"Yeah, well, you didn't come to see me off with the others," replied Daniel, "so I didn't think you wanted to say goodbye."

Vala stopped in front of him, close enough to make him uncomfortable, but not enough to cause him to back away.

He wasn't expecting the extremely hard slap that connected with his left cheek, sending his glasses askew. He rubbed his cheek with one hand and repositioned his glasses with the other. "Ow! What was that for?" he shouted as he glared.

He _really_ wasn't expecting her to take hold of his face (including his sore cheek) with both her hands and kiss him on the lips, hard. Surprise prevented him from stopping her.

She pulled back. Daniel, eyes locked with hers, repeated, though more huskily, "What was that for?" Before she could answer he realised that he was gripping her elbows, keeping her body inches from his own. He quickly let go but Vala made no move to create more distance between them. Instead she moved even closer and he felt her breath by his right ear as she whispered, "I'll miss you."

With that, Vala Mal Doran stepped back, turned and sashayed to the doors. As they opened, she looked back. He could see her eyes were glistening with tears. "Goodbye, Daniel."

Daniel, in something of a speechless daze, raised his hand to wave as she walked out. The doors automatically closed behind her. He stayed rooted to the spot for a few minutes, hand still up. Did that just happen?

But, Daniel knew he would miss her as well. A lot more than he thought he should. Over the last three years or so, she had proven herself and she had grown on him, to the point that he would notice the lack of her presence.

It wasn't that he had trouble with comprehending his own emotions. Unlike some of his friends, he usually knew what he was feeling. However, when it came to Vala he was often just confused. She got on his nerves but he liked having her around. He hated how she flirted with him all the time but there were pangs of jealousy when he saw her do it with anyone else. What did this mean?

Perhaps John Sheppard was not the only one keeping his feelings to himself. Perhaps some distance would allow Daniel to work out everything that was going on in his head. And his heart.

John stood in front of the Ancient control chair, suddenly nervous about sitting down in it. This was it. It was time. All repairs had been completed, all three ZPMs were online and the entire area surrounding Atlantis on the ground, in and on the water and in the skies were heavily guarded by all factions of the United States military. Everything was ready.

Except for John himself. Flying the city all the way back to New Lantea was a huge task. Sure, he had flown the city before, but that was a relatively short trip from one planet to another in the same galaxy, and, as he recalled, it was disastrous. Almost anything that could have gone wrong did go wrong. Plus, he lost Elizabeth.

Now, everyone expected him to just sit down in this chair, close his eyes and fly Atlantis home. As if it was that easy. No one understood what he had lost last time.

Three weeks of flying a spaceship the size of a city through hyperspace from one galaxy to another would be a challenge for anyone. Hell, he wasn't even the one who brought Atlantis to Earth. That was Carson Beckett (using the highly experimental but far quicker wormhole drive). And now that he and Keller were jointly in charge of the Infirmary (their official titles being Joint Chiefs of Medicine and Medical Investigation), Beckett was just too busy re-establishing himself as a permanent member of the senior staff. But, maybe he could help out. McKay said that once they were in hyperspace, he could leave the chair and only go back if there were complications. That didn't sit well with John, it seemed to make more sense to him to have someone in control of the chair until they were home. Maybe Carson, Lorne, himself and – no, not McKay – could take turns. They were the ones most proficient in the use of the ATA-activated technology. Then he would make the landing.

He became aware of a presence beside him. Turning his head, he noticed Rodney standing next to him, tapping the screen of his tablet.

"Aren't you going to sit down, Colonel?" he asked. He sounded more irate than usual.

"Are you sure the star drive is ready for this?" John queried, trying his best to hide his nerves. "I mean, we're talking about a long trip here."

Rodney stopped tapping and looked at John. "Of course it's ready," he answered impatiently. "Everything's ready, so let's go already!" He gestured to the chair before them.

"And why is it we can't use the wormhole drive?"

Rodney rolled his eyes. "Not this again. Look, the wormhole drive will get us there faster but it will severely deplete the ZedPMs, possibly to the point where they are completely drained by the time we get back, maybe even before. So, we do it the old fashioned way – so to speak."

John licked his lips and slowly descended until he felt the seat beneath him. He glanced up at McKay. "Are you absolutely sure that –?"

"Oh, come on, just get on with it!" snapped the scientist.

He sat back in the chair and it lit up. Immediately, John's mind was filled with Atlantis as he became aware of all its systems and its state of readiness. Rodney and his teams had done a good job of fixing up Atlantis – the city felt in better condition than it ever had before.

Zelenka had already input the course, all he had to do was follow it. He reached out with his mind and found the navigation system. He discovered Zelenka's course, then opened up the star drive and engaged it. The city rose, the cloak still activated so no one outside could see it. He knew Rodney was monitoring the altitude along with the Control Room. At the appropriate moment, Rodney ordered that the cloak be switched to the shield.

As they left the upper atmosphere, John mentally gasped as mind's eye saw the beauty of the space surrounding them. Earth's moon was visible and the Sun was in the distance. It was breathtaking. Although he had flown many ships in space many times now, this was different. It was as though Atlantis was connected to the space around it and he was connected to Atlantis. He made himself concentrate on the plotted course and followed it exactly. As they reached the edge of the solar system, John activated the hyperdrive. He saw the hyperspace window open ahead and guided them towards it. Once they entered hyperspace, he smiled.

They were going home.


	10. Chapter 10

**Chapter 10**

She kept her eyes fixed upon the man on the arid ground before her. Unknown to her, yet also known very well, she wanted to make sure she was the last thing he saw. He was all but dead.

The man was looking at her through half-closed eyes. He seemed to be trying to smile. "You look just like her," he whispered. She wasn't sure if he had actually said the words but she heard them nevertheless.

"I know," she whispered back. "Don't worry, you'll see her soon."

She then saw his gaze shift to somewhere over her right shoulder. Despite being so close to death, she noticed a familiar twinkle in those hazel eyes. "There you are," he said. This time she knew he hadn't spoken aloud.

She smiled at him but did not look around to see the person waiting for him. That was for him only. However, she could feel the presence behind her, sense the heavenly glow. She saw the light fade from his eyes and his body stilled, a very slight smile on his dirty, bloody face.

It was over. The presence behind her faded and she was alone in this godforsaken desert on Earth. Smoke and fire surrounded her but she did not feel the heat.

She looked down at the man she was with. He was so different from the man she knew. He had been broken by the life he led and was selfish and deeply flawed. But when it had come down to it, he gave his life to save others, just like the John Sheppard she remembered. Tears rolled down her cheeks as she wept for a man who lost his soulmate but found her again in death. It was still surprising to her that, although she was no longer human she could still feel emotions, as raw and as sharp as before.

Elizabeth stood and looked up to the perfect blue sky, marred as black smoke billowed overhead. She could feel the large groups of people, military and civilian, heading towards the location, both by car and plane. She knew she was smiling a little as she felt Rodney McKay amongst them. Part of her wanted to stay, to see him again, even though he wasn't "her" Rodney. She didn't even have to be corporeal or visible to do it. But when she had arrived, she had vowed to stay only until John had passed. She didn't want or need to see what happened next, what they did with his body.

Her presence in this reality was not an accident. After her Ascension she had gone to find Atlantis. It was no longer on New Lantea. She reached out and found the great city was on Earth. She wanted to go and see it but decided to wait. Returning to Earth was not something she was ready for. She would go at some point, but not yet.

So she decided to investigate why Atlantis had gone to the Milky Way. It was an exciting way to practice her newly acquired skills and when she had travelled back in time, she saw the moment the Wraith message had come through the tear in reality to be picked up by the Super Hive ship. Reaching out carefully, she realised she was able to cross over into the reality from which the signal came.

She arrived just as the fighter jets destroyed the area and found Detective John Sheppard shot and dying. It was amazing to her that she could just look at him and see everything he had been through in his life.

Her solemn contemplation was disrupted by a feeling that filled her with joy. It was coming home. Closing her eyes, she reverted to Ascended form and thought of New Lantea in her original reality.

She arrived just as her city came out of hyperspace over the planet. It was extraordinarily beautiful, the lights of the towers on and the shield gleaming against the dark backdrop of space. How she had missed it. She glided beside it as it entered the upper atmosphere, keeping invisible so she wouldn't be detected.

It took only a moment for her to realise two things. The first was that John was in the control chair. The second and far more disturbing fact was that the city was coming in too quickly. John needed to slow down.

Without any care for the consequences, Elizabeth entered the city and passed through the towers and walls until she reached the Chair Room. John was indeed in the chair and his eyes were closed. But Elizabeth could feel the tension coming off him in waves. He was anxious about getting it wrong.

Elizabeth knew that the use of the Ancient device he was sitting in now meant that one's mind was more open (though she did not know how she knew that). She floated towards the chair and positioned herself just beside John's left ear.

"SLOW UP!" came the piercing shout of Rodney over the PA system.

Elizabeth couldn't help but giggle with glee at the sound of her old friend's voice, no matter how panicked it sounded. She turned to John. He was doing his best but the memory of the last time he landed the city was dominating his thoughts.

She whispered in his ear. "John, it's all right," she started. "Just calm down."

Instantly, she noticed a change. His breathing slowed as his mind cleared and he could only see the ocean they were heading towards.

"Now, slow down," Elizabeth breathed.

She felt the velocity of the city slow as it went from what seemed almost like falling to gliding. _Thank goodness for inertial dampeners,_ she thought.

The city came to a stop just above the water. Elizabeth spoke one more time. "It's okay. You can put her down now."

John did as he was told. Setting Atlantis down, Elizabeth could feel the ripples of the ocean burst forth. She beamed. Her people were back. And she had no doubt that soon they would be causing their own ripples across the galaxy.

She couldn't stay though, as much as she wanted to. She could already feel that she had drawn the attention of the others. So, in spite of the strong urge to touch him, to tell him everything, she moved away from John and away from Atlantis. But now that she had touched his mind, she knew that she would be able to feel him wherever she was.

John opened his eyes and sat up, the light of the chair blinking out as he did.

He knew what it felt like but he couldn't explain it. The feeling was gone as soon as he straightened up.

"Elizabeth?" he said quietly, the sudden sense of loneliness breaking his heart all over again.

Teyla carefully made her way towards the Infirmary. Every corridor was a flurry of activity as people were unstrapping various items of equipment and furniture, while others were carrying out repairs. The repairs were only minor though as Rodney was happy to tell her that, apart from the early part of the landing, the journey went spectacularly well.

As she entered the office off the Infirmary, Carson and Jennifer were locked in quiet conversation. She hated to interrupt them but it could not wait. "Excuse me?"

Both doctors turned around and smiled pleasantly.

"Teyla!" Carson exclaimed. "I thought you would already be on New Athos. What brings you here?"

"I shall be leaving shortly," replied Teyla, almost giddy with anticipation. "However, I was hoping I could impose on one of you."

"Sure," Jennifer said. "What do you need?"

"I hoped one of you would be able to come with me to New Athos," explained Teyla. "Just to take a look at Torren and any others who may require your skills. It has been some time since they had access to your medical care."

Beckett jumped in just before Keller. "I'll come, love," he said sweetly. "Let me just get my kit." He wandered off.

Jennifer walked over to Teyla and put her hand on her arm. "How are you doing?"

Teyla smiled at her. "I am very excited. I have missed Kanaan and Torren very much. I …" Her smile faltered.

Jennifer's expression clearly showed her concern. "What is it, Teyla?"

Teyla shook her head. "It is nothing." Jennifer only squeezed her arm. "I do not know why but I am also quite apprehensive."

"Really?"

Teyla sat on the chair vacated by Carson. "I have been having dreams. Different dreams."

Jennifer sat next to her. "What are they about?"

Teyla inhaled and slowly let the breath out. "In one dream, Torren does not recognise me and cries when he is near me. In another, Kanaan has taken another partner because I was away for so long. In another –" she paused, looking to the woman beside her and knew she would understand. "In another, I arrive to find everyone is missing again."

Jennifer gasped quietly. "I'm sorry," she said. She was silent for a moment and Teyla could see she was thinking carefully. "You should ask Ronon to go with you as well. Say what you want about Carson, but he's not the first person I would choose to have with me in the _highly unlikely_ event of things going wrong. Couldn't hurt to have some backup."

Teyla laughed a little. "Perhaps you are right."

"Are my ears burning?" Carson said lightly as he re-entered the office and put his large backpack down.

Teyla was about to ask why he was asking them about his ears when he would be the one to know if they were burning or not but Jennifer got in first.

"Yeah, we were just saying that Teyla should bring Ronon as well as you." She grinned slyly.

"Whatever for?"

"Because he's better than you," answered Keller. She waited for Beckett's face to contort in confusion. "At shooting bad guys."

Doctor Beckett breathed a sigh of relief and laughed. "Aye," he said, "you're not wrong." He turned to Teyla. "The more the merrier."

Teyla felt calmer having spoken to Jennifer. She was right that it was unlikely to happen again but her suggestion of bringing Ronon just in case was a comforting one. As she walked along the hallways, Carson managing to keep pace with her , she contacted the Satedan who agreed to meet her in the Gate Room.

She was surprised by the sight that greeted her as she approached the Stargate. "Colonel?"

John acknowledged her with a small smile and nod. He was in full tactical gear, including the P-90 attached to his bulletproof vest. "Ready?"

Teyla was almost unable to speak. He had been avoiding her for such a long time now that his presence now was quite strange. "What are you doing here?"

John shrugged nonchalantly. "I was with Ronon when you called. Thought it would be better for both of us to be around – not that you're going to need the firepower anyway." He then seemed to sag a little. "If you want me to come, that is."

Teyla walked to him and put her hands on both his arms. Understanding what she was doing, John bowed his head until their foreheads were touching. Teyla then looked up at him. "I would be glad for you to come."

Colonel Sheppard walked behind the others as they made their way towards the Athosian settlement. He needed to walk a bit slower anyway, his legs were still aching from sparring with Ronon, who seemed to be taking great pleasure in what seemed dangerously close to torturing him today.

John was not someone who was in tune with the feelings and emotions of others but he would have had to be completely dim to not notice how Ronon and Rodney were acting towards him. He had made the decision not to confront either of them about it because he didn't want to tell them the real reasons for what was going on between himself and Teyla. He also understood their behaviour. If he were in their position he would be as angry as they so obviously were. He made a mental note to thank Teyla for keeping his secret.

However, despite the advanced knowledge of the beating he would get from Ronon, the truth was John had asked to train with him to take his mind off what had happened as he was landing Atlantis on New Lantea.

His fears of the landing had been coming true. Then, all of a sudden, he felt a presence. Like she was right there beside him. It had soothed him and allowed him to focus. He had never felt more at peace in his life as he did in that moment. He thought he could hear her voice whispering softly to him, though he couldn't be sure of the words being spoken now. And then it was gone and he felt empty.

He refocused on the path through the trees as he saw the settlement ahead of them.

Teyla, usually one of the most reserved people John had ever known, broke into a run. Everyone else quickened their pace just in time to see her reach Kanaan who was holding a young child. The boy seemed to have a lot more hair on his head and doubled in size since the last time they saw him. Kanaan's face was a mix of shock and joy.

John smiled as he watched Teyla take her son in her arms and hug him, tears streaming down her face. He would always feel some guilt for the way he had treated her the last nine weeks but Rodney had made it clear to him that she was not alone. He was glad of that. The urge to tell her everything was strong and he was wary of the fact that she had been dealing with the absence of her family.

Now, seeing that family reunited as the other Athosians gathering around to welcome their leader back, John was happy to have been allowed to witness this.

He watched as Teyla and Kanaan kissed – something he had never seen before –and was inevitably pulled back into his internal fantasies. His reunion with Elizabeth, the moment he would tell her the truth, their first kiss (well, the first one that was not instigated by aliens who possessed their bodies).

Of course there was no guarantee that things would go the way he wanted them to. It seemed almost impossible to him that a woman like Doctor Elizabeth Weir would feel the same for him as he did for her. Her last boyfriend was a successful medical doctor. He was just a soldier. But, since General O'Neill had authorised the mission, John had made sure to keep his fantasies positive.

However, the time was approaching. Now that Teyla was bringing her family home, he had to prepare to tell his friends about the mission and ask them all the biggest favour he had ever asked anyone.

Three days later, John stood in Rodney's laboratory staring at the faces of his friends who waited patiently for him to speak. It was late at night and almost everyone had turned in. Only himself, McKay, Ronon, Teyla, Lorne and Jackson were up. Well, in this room anyway.

He had played this conversation out in his head so many times. He would tell them the plan, state clearly that participation was voluntary and watch proudly as everybody's hands shot up. But, now the time was here and he found himself at a loss for words.

McKay sighed loudly and picked up a tablet. As he entered commands it started bleeping, cutting through the silence. All eyes turned to him.

"What?" whined McKay. "If he's not gonna say anything I may as well get some work done."

_He's right,_ thought John. _This is ridiculous._ "Okay, Rodney," he said wearily. "I get it."

McKay put the tablet down and John cleared his throat and rubbed the back of his neck nervously.

"Right," said John, trying to keep his voice steady. "I have a mission."

"What kind of mission, Colonel?" asked Lorne.

"A rescue mission," replied John. "A voluntary one," he stipulated.

"Who're we rescuing?" Ronon chimed in, gruffly.

John took a deep breath. "Elizabeth."

Tension descended upon the room. No one said a single word. John wished someone would say something, anything, but as the seconds turned into a minute, then two, he realised he was going to have to be the one who spoke. This was not going well so far.

"Okay, I know this is a shock, guys," he started, "but this is really something we should have done before. As far as I'm concerned."

Lorne and Teyla seemed to be the first to come out of the group stupor. "What's the plan, Sir?" said his second-in-command.

John nodded to Lorne, grateful to him for pushing the conversation forward. So, he went into the details. Getting Weir and reviving her, destroying the Asurans, taking Elizabeth back to Atlantis and helping her build a body.

He heard Rodney huff but Ronon spoke first. "So, we're going back to the original plan?"

"Well, once we get her back here, yeah," answered John. "Rodney said at the time it could work."

It was time for Rodney to finally put his oar in. "And surprise, surprise, the success of this _plan_ all rests on me." He used air quotes at the word "plan."

"Not all of it," retorted John.

"Hey, who's the one who's gonna be helping her build this body?" He paused. "That would be me, right? God, where would you be if I hadn't signed a new contract with the IOA?" John rolled his eyes. "You know, I could have gone into the private sector when we were on Earth. I had offers"

Ronon groaned. "Yeah, you've told us that before."

""More than once," added Lorne.

John focused on McKay. "Rodney, we need to do this."

"Did it ever occur to you that Elizabeth might not want us to do it?"

"Did it ever occur to you that Elizabeth might not have wanted you to reactivate those damn nanites?" John shot back.

McKay opened his mouth and then closed it again. Just as John thought he would remain quiet, he spoke again, this time defensively. "Look, I made a mistake, I know that. But, I was trying to save her life! And, may I point out that if I hadn't reactivated the nanites we wouldn't have been able to steal a ZedPM from the Asurans and we'd all be dead. _And_ we wouldn't be discussing this now!"

"Rodney, the fact is you did do it and now we're discussing this." John was doing his best to pacify him. He was integral to the success of the plan. He needed him onside. He noticed his voice sounded almost as though he was pleading. "She needs our help."

McKay stuttered as he spoke in his raised tone. "But… but, it was her idea! She did it to keep us safe!"

"If we destroy the other Replicators and keep her isolated until she can be transferred into her new body, then we will be safe. I've thought this through."

"See, I don't think you have," challenged McKay. "First of all, going on a half-cocked, unauthorised rescue mission –"

John cut in. "It is authorised!"

Rodney stopped short. "What?" he said, disbelievingly. "Who authorised it?"

"General O'Neill."

"Really?"

"Yes."

"Oh."

Teyla finally spoke. "How can we destroy seven Replicators?" she asked.

"ARGs," was John's response.

"But, will they not adapt after we have destroyed the first one or two?" she inquired.

John eyed McKay. If he was wrong in what he was about to say, the Astrophysicist was sure to pipe up. "They were only allowed the most basic bodies which means their nanites can't replicate or adapt, so we should be able to get them all."

Teyla turned to McKay. "Is John's assessment correct, Rodney?"

McKay did not break eye contact with Sheppard as he answered. "Yes, yes, he's right about that."

"That's good," said Ronon.

"What if she becomes dangerous?" demanded Rodney.

"That's not going to happen –"

"But, what if it does?" said McKay. "What if we can't make a body for her? What happens then?"

Of course, John had an idea for these eventualities. General O'Neill's contingency plan was to destroy her but John knew in his heart he could never do it. However, he was not ready to tell the others either the General's solution or his own, knowing they would have difficulty accepting them. "I have a plan for that too."

Daniel chose that moment to put his own opinion forward. He was only really here for back-up and was not going to speak unless he felt he needed to. Obviously, that time had comej. "Colonel Sheppard's right. Doctor Weir was in charge of Atlantis for three years. Wasn't she a good leader in that time?" He indicated to John. "She made John a part of the Expedition when everyone was saying it was a mistake."

He moved over to Teyla. "She helped you find out why you can sense the Wraith. That knowledge has been invaluable, hasn't it?" Teyla nodded.

To Ronon: "Elizabeth gave you a home and a purpose after being a Runner for years."

Finally, he turned to McKay. "She…put up with you, Rodney. Humoured you. Allowed you the freedom to …grow, to become as important here as you are."

He then addressed all of them. "Elizabeth Weir deserves more than to spend…what, eternity?... just floating in space. She's not dead, she's not alive. She's in Limbo. I wouldn't want that. Would you?"

Once again, John was grateful for Daniel's presence. He had managed to eloquently state the reasons why they should be doing this in a way that he could never have hoped to himself. He was dreadful when it came to eloquence and speaking from the heart. Everyone seemed to be pondering what he had said.

Except for McKay. "What's he even doing here?" he spluttered. "He wasn't even around when Elizabeth was here!"

Daniel turned to Sheppard but said nothing. "He's here because I want him here," John said, nearly losing his temper. "Daniel was Elizabeth's friend too. And he's been helpful in figuring out the mission."

"What?" shouted Rodney. "You told him before us!"

Sheppard took a slow deep breath, trying to find his centre. He wasn't sure he had one anymore. "That's not the point, Rodney."

"And friends? He barely even knew her!"

"Not that it matters, but I overheard John's conversation with Jack," said Daniel who had taken off his glasses and was rubbing the bridge of his nose. "Besides, I knew Elizabeth and worked with her long before you even met her." Daniel turned slightly red and looked down, visibly embarrassed at being drawn into a childish row. John sighed. He wished he could say that McKay had never done it to him before.

"Look, Rodney," said John, his voice sounding so much calmer than he was. "This is voluntary but I can't carry out the mission without you." He looked at each of his friends. "So, I am going to ask if you want to volunteer."

The first hand to go up was Lorne's, followed closely by Ronon and Teyla. Even Daniel, who knew he wasn't part of the team John had lined up, raised his hand.

Rodney looked at them all, then back to John. John thought he could see the man's eyes glistening. "I… I need to think," he said quietly and left the laboratory.

John lowered himself on to the nearest stool by the table they were sitting around and laid his head down on the table. He resisted the urge to bang his head on it – repeatedly.

He needed Rodney McKay. Without him they could only carry out Phase One – destroying the Replicators - of the plan. Phase Two – reviving Elizabeth – would probably require his expertise and Phase Three definitely would.

He got up. "Thanks, guys," he said, hearing the flatness in his tone. He walked out without another word.

He had only reached the end of the corridor when he felt a hand on his arm. He turned slowly to see the sympathetic smile of Teyla.

"Why did you not tell me?" she asked softly.

John looked down at the floor. "I wanted to but General O'Neill wanted it to be top-secret until we got home. He didn't want the IOA to stop me." He made eye contact and spoke sincerely. "I am so sorry I wasn't around lately, but I knew I wouldn't be able to keep it from you. You know the truth."

Teyla smiled serenely as a tear rolled down her cheek. "I understand now. And I can see why you have been so much happier recently."

"Yeah, well," mumbled John, "doesn't matter now."

"Go talk to him," advised Teyla.

"What do I say?" asked John.

"Tell him the truth," she replied.

John snorted. "Yeah, okay, that'll work."

"You never know."

John did his best to smile. "Thank you, Teyla." He turned and walked away.

* * *

In his quarters, Rodney McKay was distracted from his pacing by the sound of the door chime. He ignored it.

What the hell was Sheppard thinking? Bringing a Replicator to Atlantis? Expecting him to perform a miracle by giving her a human body? What could he have possibly done over the last five-and-a-half years to make Sheppard believe he could do something like this?

The door chime sounded again.

_Oh, right. Save the team countless times, save the city nearly as many. Save the galaxy a few times too._ Damn, why did he have to be so brilliant?

The door chimed for a third time. He wasn't going to go away, was he?

He stomped to the doors and all but slammed the panel to open them. Sure enough, John Sheppard stood there with his stupid messy hair and his stupid sad eyes.

"Can I come in?" he asked timidly.

Rodney considered saying no. After all, he had told Sheppard he needed to think. Coming to his room, less than fifteen minutes later did not give him nearly enough thinking time – not for a brain as big as his that could calculate hundreds of different scenarios in a short space of time. Okay, maybe he could see why he was here already. He stood aside, allowing the Colonel enough room to get in, then waited for the doors to shut behind him.

John stood before him with his hands in his pockets and staring at a fascinating spot on the floor. He said nothing.

"I'm still thinking," Rodney opened with.

"Okay," said Sheppard. "So, it's not a no, then?"

Rodney let out an exasperated sigh. "Not yet." He decided that since Sheppard was here, he should ask what was on his mind. "What makes you think it's a good idea to bring her to Atlantis?"

"She's Elizabeth, Rodney," answered John. "You said so yourself."

It was true. Until the entity in F.R.A.N's body had stepped through the event horizon and signalled her fellow Replicators that all was well, Rodney had been unsure it was Elizabeth. However, despite the uncertainty, guilt had overruled his head and he tried to help her. It had taken her sacrifice for him to see he had been right but by then it was too late. After that, it was like he had shut a part of his memory away – anything to do with Elizabeth was hidden somewhere that wouldn't affect his peace of mind, because if he thought about her and how she ended up, he would probably go crazy.

"Were you planning to leave her there forever, Rodney?" John was looking at him curiously.

"I… I don't know," stammered Rodney. "It was what she wanted."

"Do you really believe that?" When Rodney remained quiet, he added. "It wasn't what she wanted, it was something she had to do to get the Replicators away from Atlantis."

Rodney could see what he was saying and was mentally kicking himself.

John continued. "Now, some time has passed, hopefully, Elizabeth is far enough away from the space gate to not be hit by a jumper and we can deal with those Replicators permanently. Once they're no danger, there isn't any reason why Elizabeth should stay there."

Rodney nodded, having heard Sheppard's explanation but still stuck on what he had said before. Who would want to spend forever floating in space? Especially when you can never die? Why had he not considered that before? Had he been so disturbed by everything that had happened to Elizabeth that he had put it in a box, topped off with the platitude _"It was what she wanted" _and forgotten about her. It was despicable.

His train of thought was disrupted by Sheppard's intense stare. "What?"

John narrowed his eyes. "Why do you have such a problem with this mission?"

Rodney shook his head vigorously. "I don't," he countered. "I just…" He stopped. He knew what the problem was but it was difficult to describe without sounding completely mad. "Un…I guess… I don't want to be disappointed again." He paused to see John's head nodding slowly. He spoke quickly to qualify his response, foregoing the need to breathe in order to get it all out. "We've been here before, you know, we get her back and we're happy – or in the case of last time, incredibly suspicious – but we try to help and then we lose her again. And if it happens again I think I'll lose it." His shoulders dropped as he finished.

Sheppard exhaled. "I know what you mean, Rodney."

"You do?"

"Course I do," John reiterated. "I felt it every time too. It won't be like that this time though."

Rodney's eyes widened as the implications of all that they had been discussing led him to an awful realisation.

Sheppard walked towards him. "Are you okay?"

Rodney looked up at him. "I'm a bad friend," he almost whispered.

Sheppard instantly turned away and he spoke, almost distractedly. "Why would you say that?"

"I turned those nanites on when she wouldn't have wanted it, I let her leave that jumper on Asuras, I assumed she wanted to go through the Stargate and stay there and I didn't want to hear your plan because _I_ didn't want to be disappointed again! I'm a terrible friend!"

John hesitantly brought his hand up. Unsure what he was about to do, Rodney was relieved when the hand went to his shoulder, patted it once and then hastily returned to its pocket.

"You're not a bad friend," placated John. "You were trying to save her life, you couldn't have stopped her leaving the jumper if you tried and you were trying to follow her wishes." He sighed and sat on the bed. "I left her behind. I believed she was dead because an Asuran-created clone told me and I made her sacrifice herself."

"You made her?"

"I told her she wasn't Elizabeth anymore," John confessed. "Next thing I know she's saying they have to go and she has an idea."

"Oh." Rodney sat on the bed beside John. "Guess we both could have been better friends."

John chuckled humourlessly. "Yeah," he agreed.

"Is that why you want to do this?" asked Rodney.

"Pretty much," said John. "But she deserves another chance, don't you think?"

Rodney smiled. "Yeah, I do." He turned to his friend. "I'm in."

John's eyes lit up. "Really?"

"Why not?" Rodney shrugged. "We help our friends, don't we?"

John practically jumped up from the bed. "We do. I need to talk to Woolsey."

Another thought hit Rodney, as they often did. "John?" Rodney called before he reached the door.

John stopped and turned around.

Rodney stood and started wringing his hands, nervous about what he was going to say. "There's one thing, though."

"What is it?" John asked, cautiously.

Rodney looked down at the floor. "What if I can't do it?"

"Of course you can –" John started.

"But what if I can't?" cried Rodney. "This is Elizabeth. Will they let her stay if I can't make a body for her?"

John was silent for a moment before replying. "No."

"Oh," he said sadly. _No pressure then_. He had to create a body for her, he just had to. He couldn't let her down again. He couldn't bring her home and then fail to save her. He had to –

"Wait a minute!"

"What?" said John, startled by Rodney's sudden exclamation.

Rodney pointed at John and noticed his finger was shaking. But he felt the excitement growing in the pit of his stomach. Sheppard could be a bit of a genius himself. And he had just remembered what he said in the lab. "You said you had a plan for that possibility."

John turned away again. "I did," he said quietly.

"Well, what is it?" Rodney asked, hands gesturing impatiently.

"It doesn't matter right now," said Sheppard.

"What does that mean?"

"I don't want to discuss it," he almost growled.

The excitement turned to dread. "John?" he implored as he walked towards him. "What are you going to do?"

John looked at him and Rodney could see something in his tired eyes. He had seen it before when they had been in danger and he was considering something stupid. "Oh, God, are you going to kill her?"

"No!" John shouted quickly.

"Then, what?"

John looked up at the ceiling. "Fine, but you tell no one." His finger was raised as he spoke with a warning tone in his voice.

Rodney nodded, the dread deepening.

"If we can't give her a body or if she becomes dangerous, then she'll go."

"Okay…"

"And I'll go with her."

"What?" Rodney unintentionally screeched. When Sheppard didn't say anything, Rodney regained his control and reasoned, "You mean you'll go with her until she's somewhere safe and then you'll come back. Right?" Why was his voice trembling?

"No."

"So… you're… what?"

"I'll take her in a jumper and we'll go together. I'll take care of her."

"Why would you do that?" Rodney asked, trying to keep himself in check. He was torn between screaming in anger and crumbling. "Because you feel guilty?"

John shook his head. Rodney looked him in the eyes and could see tears forming. _Wow, never seen that before._

"Then, why?"

John held his gaze and swallowed, seemingly wrestling with something. Then he spoke so quietly, Rodney wasn't sure he heard him correctly. "Because I love her."

He loved her? John Sheppard loved Elizabeth Weir? "Kirk" loved Elizabeth? Rodney felt as if his incredibly large brain was about to haemorrhage. It didn't make sense. Colonel John Sheppard was a typical flyboy, love-'em- and-leave-'em type. Elizabeth was so far off the scale of his normal type. She was strong, intelligent, and beautiful in a natural sort of way… and not an alien or an Ancient. Rodney would even go as far as to say she was out of his league – but not to his face.

His memory tried to find any clues that would show him he had missed something. There was obviously the kiss but they had both been possessed by aliens at the time. But Rodney remembered being surprised at how it didn't look weird to see them kissing each other. Why wasn't it weird?

There was the way they would watch each other and in briefings, sometimes, it was like they had entire conversations without a word being exchanged. That had freaked him out in the first year, but then he got used to it.

He brought her coffee. Every morning, he would bring her a cup of coffee for the briefing. But not anyone else, only Elizabeth. Rodney always had to get his own, much to his chagrin. Maybe he should have been glad that John didn't bring him coffee.

Sheppard broke the quarantine when Elizabeth was first infected with the nanites. He didn't leave the Infirmary the entire time she was unconscious, even though he was supposed to be in charge of Atlantis in her absence.

He had talked with Teyla, Ronon and Jennifer about the change in John's behaviour in the last couple of years. He had obviously been upset about leaving Weir behind but the real change came when Elizabeth had gone for the second time. After that, he never seemed happy, never seemed like himself.

In fact, if Rodney thought carefully, John's suicidal plans seemed to become pretty frequent after she went through the Stargate to her fate.

_Oh my God, he loved her!_

Rodney regarded his friend again for a moment before his thoughts overtook his focus once again. Now, he didn't see an Air Force flyboy with a crazy plan. He saw a desperate man with a mission to save the woman he loved. He wanted to talk John out of leaving, but found that he could not. He would do the same thing if it were Jennifer. John Sheppard had given so much. He deserved to be happy. They both did.

He was snapped back to reality by the sound of the doors opening. "John, wait!"

He ran to the doorway to see Sheppard had stopped just outside in the hallway. He looked back but couldn't make eye contact. Rodney felt guilty. It must have seemed like he wasn't even paying attention to him, like he didn't care.

"Don't worry," Rodney got out. "I'll figure it out."

"Thanks, McKay."

"You really love her?"

"I do."

Rodney smiled. "You know, you would make a cute couple."

John's eyes locked onto his. "You think?"

"Yeah. Not as a cute as me and Jennifer, though."

With that, John Sheppard walked away, seemingly taller than his actual height. Rodney walked back into his room and picked up his tablet. He would start with Michael's cloning research. Perhaps combining this with Elizabeth's knowledge would speed up the process.

He left his quarters, heading back to his laboratory. It was late, but so what? He had two friends to save.


	11. Chapter 11

**A/N: **Hi everyone, hope all is well. I just wanted to thank you all for reading. The one thing I said to myself before I started this was that I was doing it to get my story out there, not to see what people thought of it. But, I have to admit that I love reviews. So I just want to thank you for posting them and ask that you keep doing so.

**Disclaimers:**Two this time. One for the characters, etc. of Stargate:Atlantis. Not mine. Never will be. My other disclaimer is for a particular song that has been used in this chapter. Not mine, no copyright infringement intended.

And on we go...

**Chapter 11**

The leader of the Atlantis Expedition was not a fighter. He could barely fire a gun and his hand-to-hand combat skills meant that running away was always the better option. He was an intelligent man but he was not a genius astrophysicist like Doctor McKay or a military strategist like Colonel Sheppard.

Richard Woolsey's original calling had been the Law. A graduate of Harvard, he was seen as something of an artist by his peers: the courtroom was his canvas, the Law his watercolours. This work had led him to the NID and, eventually, the IOA.

But, while he was not a violent man or an overly smart one, he did like to think that to be leader of an expedition composed of civilians and military, of different nationalities and egos of varying sizes, you had to be a people person. Well, somewhat anyway. Richard would be the first to admit he was no Elizabeth Weir, but he liked to think he had his finger on the pulse of Atlantis. He respected these people and they respected him. He knew when they needed a push and when to leave them alone.

However, one thing he was never certain about was his second-in-command. Colonel Sheppard was a good man. He was not someone Richard would have chosen to be part of the Expedition, given his prior record, but he would have been wrong. Back then, he relied very little on his instinct. Doctor Weir trusted hers and chose to bring Sheppard, despite the warnings. She had been correct of course and he couldn't imagine someone else as the military commander in Atlantis. The Colonel had shown him that rules were all well and good – until someone else decided not to follow them. And that happened frequently in the Pegasus Galaxy.

When he first met him, he found John Sheppard to be a passionate but rather argumentative man. He was very protective of Doctor Weir and her leadership and evidently did not appreciate Woolsey's assignment to audit her role and decisions. They did not interact much in later visits until Richard was installed as leader. The Colonel still cared about the city and its people but he was not the same as the first time he encountered him. There was less passion, more distance and a bubbling anger.

That had altered recently. Colonel Sheppard seemed to have changed somehow, though Woolsey could not name any one indicator in particular. He just knew he was less angry.

Richard watched as the man in question stood in the Control Room, near the bridge to his office. He had been standing in the same spot for forty-five minutes. He did nothing else but look towards the office. It was beginning to draw the attention of the technicians.

It was obvious that Sheppard wanted to talk to Woolsey about something, but he just wouldn't cross the bridge. Woolsey had been waiting but his patience was wearing thin.

He tapped his earpiece. "Colonel Sheppard." He kept his eyes on his tablet.

The response was immediate. "Sheppard here."

"I need to see you in my office, ASAP."

"On my way."

Richard continued to read an especially long e-mail from Doctor McKay as he waited.

There was a timid knock on the glass pane moments later. Woolsey glanced up to see Colonel Sheppard in his usual all black uniform of trousers and untucked shirt with the sleeves rolled up, in the doorway.

Woolsey indicated to the chairs on the other side of his desk. Sheppard sat in the one to the left but did not seem comfortable as he shifted around. Woolsey again waited until he stopped.

"Now, is there a particular reason you've been loitering in the Control Room for nearly an hour?"

John's head lifted to meet his eyes. "You saw that, huh?" he said sheepishly.

"I did."

Sheppard licked his lips. "Okay, I need to tell you something."

"You do?" Why did he have a bad feeling about this?

"General O'Neill has authorised a mission." He stopped there.

Woolsey blinked in surprise. A mission had been authorised without his knowledge? Why had he not been informed? Or conferred with? He tried and succeeded to keep his voice neutral. "Do tell."

Colonel Sheppard was not normally so hesitant and overtly nervous. "Um… okay." He cleared his throat and straightened up. "Our mission is to take a puddle jumper through the 'Gate to where we sent Doctor Weir and the Replicators. Once there, we destroy the Replicators and bring back Doctor Weir." He paused, as if waiting for Woolsey to say something. Woolsey was too busy trying to keep his jaw from hitting the desk. So Sheppard continued. "We then keep her isolated whilst she and Rodney's teams build her a human body."

Richard remained quiet. He was unsure as to how to respond to the bombshell the man before him had just dropped. General O'Neill had authorised this? He was surprised. He knew O'Neill to be a man who sometimes followed his heart, but at the expense of the safety of Atlantis? "I take it this is why you saw General O'Neill as the SGC after your debriefing."

"Yes."

"I see." There was silence. Richard was hoping for Sheppard to give him some kind of explanation but he said nothing. "May I ask, why now?"

Sheppard squirmed. "Honestly, being back on Earth with Atlantis just reminded me of the fact that she wasn't there. And I realised that Doctor Weir's situation can be…"

"Rectified?" Woolsey offered.

"Right," agreed John. "Elizabeth's not the real danger to Atlantis, the other Replicators are and the longer they're left out there, the more chance of someone finding them – maybe even the Wraith. And I don't think I need to tell you how bad it would be if the Wraith got a hold of Elizabeth with the knowledge she has."

Woolsey nodded. That was very true. Sending the Replicators through to the Space Gate was, at best, a temporary measure. Why was he so surprised that Colonel Sheppard had come to him with a more permanent solution? A solution that included salvation for Doctor Weir. The only real surprise was that it had taken Sheppard this long to mount a rescue.

However, it somewhat hurt that Sheppard had not come to him first. Instead, he had gone over his head and straight to the Head of Homeworld Security. Well, he was not one to keep things to himself. "Is there a reason I was not included when you spoke to General O'Neill?"

He noticed Sheppard fidget in his chair even more and swallow before he answered. "I… thought the IOA would deny any request for a rescue attempt… I know how they felt about Elizabeth."

"That's the IOA, not me." He remained calm.

"And you work for the IOA – you would have had to contact them," answered John.

Woolsey leaned back in his chair and sighed. "I thought that by now I had proven that I am not merely the mouthpiece of the IOA – not that I should have to prove anything. I thought we trusted each other by now."

"I trust you!" Sheppard insisted. "That's why I'm telling you now."

"But you didn't trust me before. You went over my head, Colonel." He took off his glasses and rubbed his eyes as he felt a headache beginning to form.

Sheppard slumped in his chair. "What would you have said if I had come to you first?"

Woolsey knew the answer to this and said it as confidently as he could. He wanted the man across from him to know he was serious. "I would have said yes." He put his glasses back on.

John's face was a picture of pure shock. "You're kidding, right?"

"I think you know me well enough to know that I rarely kid about such things." He paused. "Or anything, really."

Colonel Sheppard smirked. "Why?"

"Why, what?"

"Why would you have said yes?"

Richard almost rolled his eyes. "I would have thought that obvious, Colonel," he replied. "Doctor Weir shouldn't be out there and if we can give her a human body then it's the right thing to do. Everyone here liked her a great deal. They still do. Morale would increase among the staff." He stopped. "I know that when we first met you were concerned that I was trying to find reasons to remove Doctor Weir from Atlantis. But the truth is that I respect Doctor Weir a great deal and would be glad to welcome her back." Everything he said was true. Everybody would be pleased to see her return.

However, Sheppard was probably right that the IOA would have a problem. Well, screw them! This was right. Plus, the security threat represented by the Replicators and Doctor Weir, if left there was certainly real. But Richard knew it weighed heavily on his second-in-command that he had not been able to help her. And after all he had done for Atlantis, for the Pegasus Galaxy and for Earth, maybe he had earned the right to do something that he wanted to do. Something that would help him achieve some semblance of peace.

Sheppard had said nothing. He still seemed to be processing Woolsey's words. Finally, he spoke. "Thank you, Mr Woolsey." He cleared his throat as his voice was raspy. "I'm sorry. I-I should have… trusted you… before." He looked down.

"Well, it's done now," said Woolsey kindly. He didn't want Sheppard to feel _too _guilty but he did want to know more. "Tell me the plan and what you need."

* * *

John knew that he was whistling as he took the well-trodden route to Rodney McKay's laboratory. He didn't even care. Let other people hear him. So what? Life was good.

He was glad, if somewhat surprised, by Woolsey's willingness to buy into the mission. He really believed that he would need convincing. But, not only did he agree that Operation Sedgewick should take place, he had scheduled it.

This was really going to happen. And soon. He was going to bring Elizabeth Weir home.

He walked into the laboratory and saw his friend hunched over his desktop PC. There was a pile of computer tablets to the left of the keyboard and a mug and coffee pot to the right.

He didn't look up as he spoke. "Colonel Sheppard, I recognised your foul stench when I was brought on board." He sounded exhausted.

"Funny," retorted John. "How'd you know it was me?"

"Heard your infernal whistling down the corridor," answered Rodney as he turned in his chair. Kinda distracting. What is that song by the way? It's driving me crazy."

"I'll stop then." Not that he meant it.

"No," Rodney snapped, a little too harshly. "I mean it's driving me crazy that I can't figure out what the song is."

"Oh," said John. "_Woman._"

"_Woman_?"

"John Lennon."

Rodney snapped his fingers, then pointed at him, whilst putting the index finger of his other hand on his nose. "Right, right."

"Lennon fan, McKay?" teased John.

McKay shook his head. "Jeannie."

"Of course." That made sense.

"So, why do you keep whistling that song then?"

"What do you mean?"

"Well, for a start, it's not Johnny Cash."

"I do know songs that aren't by Johnny Cash," John argued, his voice rising defensively. Realising he was about to be drawn into a row over a song, he made the decision to change the subject before Rodney could bite back. "Were you in here all night?" he asked noticing the dishevelled look and wide caffeine-fuelled eyes.

The crazy eyes turned back to the computer screen. "Yep."

"What are you doing?"

"Going over the data Elizabeth put in the computer the last time she was here – seeing what there is about creating the technology capable of building a human body and transferring a consciousness from a Replicator body to a human one," McKay stated, not turning away from the screen.

John leaned back on the high desk to Rodney's left, careful not to touch the tablets, and looked down at his friend, gratitude overwhelming him. He had been concerned during the night that telling him how he truly felt was going to be a mistake. Evidently, his fears were unfounded. The man would never admit it, but John knew that Rodney was working this hard for him as well as Elizabeth.

However, there would be time for this later. He needed Rodney at his best. "Well, make sure you go to bed at some point 'cos we have a mission tomorrow."

Rodney's head snapped up. "You mean...?"

"Woolsey's scheduled us to go at 08:00 hours." John couldn't help but grin.

"Wow."

"I know. He's even said that he'll hold off telling the IOA for as long as he can."

There was an awkward silence as the reality of their mission settled upon them both. John was terrified. Now that it was actually going to happen, the possibility of things going wrong was also a reality. He couldn't bear to entertain the chance that he would fail. He suspected Rodney felt the same way.

John straightened up from the table, preparing to go and inform the others and start prepping Puddle Jumper One.

"John?"

He looked back down to see worry in McKay's eyes. "About Plan B."

Knowing he was referring to his leaving Atlantis, John sighed. He should have known that Rodney would not be able to resist bringing that up. "What about it?"

Rodney opened and closed his mouth nervously before finally saying, "Are you sure?"

If there was anything that John Sheppard was sure about, apart from Operation Sedgewick, it was this. He knew, beyond any doubt, that he was going to be with Elizabeth. He was not going to let the chance pass him by again. Even if she didn't love him, she would need someone to watch her back, to keep her safe and, to an extent, keep others safe. He was absolutely certain. He answered assuredly. "I am."

"But…"

"But, what?"

"Well, Atlantis is your home. You're needed here."

John leaned back on the desk again and closed his eyes briefly, gathering the words he hoped would explain. He looked down at his arms which were folded across his chest. "It's funny, you know. Atlantis doesn't feel like home anymore, hasn't for a while." When Rodney remained quiet, he clarified. "Elizabeth gave me this home and it's never been the same without her."

"But you fought so hard to get the city back to Pegasus."

"Because it was the right thing to do. And because it was what she would have wanted."

"Oh." A pause. "Okay."

"As for being needed here, Lorne will be a great military commander and Carson is finally good with the Ancient tech." He tilted his head to one said. "But, if you really did need me, I would hope that I could come back to help."

Believing that he had cleared things up, John started to move towards the door. However, he heard the squeak as Rodney turned in his chair.

"What if Elizabeth wants you to stay here?"

John froze near the doorway. It was possible. It would be just like Doctor Weir to put the needs of the city before her own, even if it meant her death. However, the way he saw it, her refusal was not an option. It was his decision.

So he turned back, response ready. "I think I've had enough of doing what Elizabeth wants. She wanted me to take her to Asuras and I did. She told me to leave her there and I did. She went through that 'Gate into nothing and I let her go. I want to do what I want. And she can't be alone. I doubt Woolsey would just let her go if she was on her own. She's gonna need me, more than Atlantis." With that, John spun around and left before McKay could ask anything else.

* * *

Teyla Emmagan took a deep cleansing breath. The quarters she shared with Kanaan and Torren were darkened, only the area around her lit by a few candles. She used to use many more candles during her meditations; however, she now had a son who was curious about all that was around him.

She opened her eyes and looked to the bed by the window. Both her partner and son were sleeping peacefully. It was only afternoon but they had been very busy, exploring accessible areas of the city and stopping for a picnic on the East Pier.

Colonel Sheppard had come to see her in the morning to tell her of his conversation with Mr Woolsey. Therefore, the whole team had the day off. Teyla could see the elation on his face but she also saw the fear in his eyes. It was a fear she understood. She had felt it every day when her people were missing. Each day, she hoped for news of them, particularly the father of her unborn child, and each day she feared they would never be found.

Teyla knew that, although John was confident about the mission, he was also scared. Scared that Elizabeth would not be there, scared that she could not be saved.

"Do you wish to talk?" she had asked him.

"What about?" he replied.

"About Elizabeth," she said, her voice lowered, so others would not hear.

John did not answer for a moment and Teyla started to think that he would accept her invitation. Then he shook his head. "No, I'm okay, Teyla. It's a big day tomorrow. Have some fun with Kanaan and Torren today." He then smiled and left.

It had been a good day. She had enjoyed herself a great deal. Now, as her family rested, she took the opportunity to meditate.

However, she could not fully relax. She could not stop thinking about tomorrow, about what was to come.

Elizabeth Weir was her friend and she missed her dearly. When she had found out her fellow Athosians were missing and then shortly after, that she was pregnant, she had wished that Elizabeth had been on Atlantis for her to confide in. She would have been understanding and sympathetic. She would have most certainly been concerned about her participation in the team's activities, but she would have been happy to help in any way she could.

Teyla wondered how different things would have been had Elizabeth never left Atlantis, if she had recovered from her injuries safely or not been hurt in the first place. Would she still be in charge of Atlantis now? She had been worried that she would lose her position, but Teyla believed with all her heart that she would have fought to remain, as would everyone else in the city.

What of her relationship with John? Once Teyla was aware of the depth of John's feelings, she spent time analysing the interactions between her two friends over the years. Both were expert at keeping their emotions carefully concealed (although there had been discussions between everyone about the possibility, Teyla had sometimes participated but considered it to be nothing more than gossip). But knowing what she knew now, she could recall small tells from John that on the surface were innocent, but were, in fact, so much more. Lingering looks, small comments, touches. It occurred to her that Elizabeth displayed those same tells on occasion. The way entire conversations seemed to pass between them with a mere look, the way she would watch him as they went through the Stargate, how she would look to him when they returned. The worry she struggled to hide when he was once again in the Infirmary.

In addition to these things, Teyla remembered talking to Elizabeth when she visited her in the Isolation Room in F.R.A.N's body. She told her about her son. Upon hearing his middle name was John, she had asked if he was the father. The tinge of panic in her voice, followed by relief in her eyes when Teyla told her he was not, was quite obvious, even back then.

Teyla considered telling John her belief that his feelings were reciprocated but made the decision not to. It was not her place to reveal such information. However, had Elizabeth remained, it was difficult to imagine that either person would have let their guards down enough to allow their feelings for the other to show.

Perhaps that was the reason for what happened. Perhaps something terrible needed to pull them apart so they could finally be together. Perhaps it was all part of the Ancestors' plans.

Teyla sighed and opened her eyes. She was not going to be able to relax enough to reach a state of complete calm. She stood and smoothed down her long brown skirt. Barefoot, she quietly crossed over to the bed and climbed onto the empty side of the mattress, Torren sleeping soundly between herself and Kanaan. She gazed at them both, wondering how she ever got through life without them. She had known Kanaan since they were children but had never embarked on a relationship until two years ago. Love was something she had always known, first from her parents and then from her people. But it had never consumed her heart until she had given herself over to what Kanaan offered and then given birth to their son. This was what her life was leading to, what it had always been heading towards. She could not imagine a future without them.

She delicately placed a hand on the cheek of the man she adored. His dark eyes opened and she stared into them happily. His short black hair and well groomed beard suited his handsome face perfectly. "I did not mean to wake you," she whispered.

"It is all right," Kanaan said, his voice just as quiet. "You were not able to meditate?"

Trust him to know. "No."

"Too much on your mind," he stated.

"Yes," she confirmed.

"All will be well," he said, taking his hand from his cheek and entwining his fingers with hers.

Teyla smiled. She had not told him the details of the mission but he knew it was important to her. "I hope so."

They both looked down at the small boy between them. His skin was lighter than his mother's but his eye colour seemed to be turning to match her own. Though rather long and messy, his hair was the colour of his father's.

Teyla felt more content now lying here than earlier. Whilst she was still worried about the mission, she had hope that, one day John Sheppard and Elizabeth Weir would know happiness as she did.

* * *

Rodney's stare was directed towards the computer monitor but he didn't see what was on it.

He rubbed his eyes as they started to hurt. _God, I need to get some sleep, _he thought. He was so tired, he could no longer concentrate on what he was attempting to accomplish.

Building a body for Elizabeth was not going to be easy. He still had the schematics for the machine she and the other Asurans created the last time they were here and the laboratory they had used remained untouched. They were creating new technology at the time and circumstances meant that the new technology was now in that laboratory unfinished. At least he had a starting point. What he didn't have now that he did then were eight Replicators that required neither sleep nor sustenance. He could not even be sure of what knowledge Elizabeth retained and if she would be able to help.

It was possible that this project could take months, a year even. A year, during which, his friend would be kept in isolation. It wasn't fair. Not to her and not to Sheppard. How was it right to take her away from the isolation of space and drop her into an empty part of the city, alone, except for when she worked with the science team?

Rodney was still reeling from John's revelation last night. He knew how difficult it must have been for him to tell McKay he loved Elizabeth. Sheppard was not exactly the most forthcoming of people when it came to talking about his feelings. It was one of the few things the two men had in common. He sympathised, he truly did. He couldn't imagine how he would cope if he lost Jennifer, never mind if he lost her over and over again. McKay was surprised John hadn't lost it.

But was he losing it now? John's promise that he would leave Atlantis with Weir if they couldn't help her seemed a tad insane. He didn't even care if Elizabeth felt the same. However, it was incredibly unlikely that the IOA would allow a Replicator (even one they knew) to remain on Atlantis for a year. When they found out, and that was inevitable, they would probably put up with the situation for a few months and then she would be – what? Evicted? Destroyed – no – murdered?

If Rodney was right about that then it was likely that John would have to follow through on what he said. If it were anyone else, McKay wouldn't expect that they would actually leave Atlantis. But Sheppard would. Once that man set his mind to something, there was very little that could be done to change it – Elizabeth was one of the few people that could though. How would she feel about Sheppard's decision?

No matter how much he understood, McKay just could not reconcile himself with John's final solution. Atlantis without Colonel Sheppard was like a water molecule without the oxygen atom, like bacon without eggs. It didn't make sense in his head and he could not think of anything else since the person in question had been in the laboratory a few minutes – he looked at the clock on his monitor – scratch that, six hours ago.

Six hours. _Six freaking hours!_ And what had his brilliant brain come up with? Nothing. What had he been thinking about in all that time? Sheppard leaving. How he would miss him. How he needed to figure this out or he would lose yet another of his best friends.

"Oh, get a grip, you big girl!" he shouted at himself, slamming his fist on the table, narrowly missing the keyboard. "Focus on the problem you can fix. Forget about the other stuff."

"Excuse me?"

Rodney froze, then slowly turned his chair to the direction of the soft accented voice. Radek Zelenka, with his untucked blue top, his stubbly face and hair that looked like he had recently stuck his fingers in a plug socket, stood in the doorway, staring at him in bewilderment.

There were three ways he could go here. He could explain the situation but it was still a secret at the moment. He could simply apologise to the Czech scientist. Or he could tell him to get out and mind his own damn business.

"What do you want?" McKay demanded.

"Is everything all right?" asked Zelenka, concern evident in his tone and facial expression.

"Everything's fine!" snapped McKay. "Now, are you here for an actual reason or did you think my lab needed to be decorated with a living statue?"

Zelenka straightened up and his face went from worry to annoyance. "You know what? Forget it!" He turned and stomped out, a barrage of what McKay now knew to be Czech expletives echoing down the corridor.

Rodney breathed a sigh of relief and slumped back against the table, still watching the door. Of course there was no need to chastise Radek like that but he couldn't think of a better way of getting him out of the room before he saw what he was working on. He would probably have to apologise for it later. Hopefully, he would be more understanding when McKay made him part of the team tasked with assisting Elizabeth.

McKay briefly considered the vast number of people who worked for him. Who would be best suited to help bring Elizabeth Weir back into the fold permanently? Who would work accurately but with speed so that she and Sheppard wouldn't have to leave?

He marvelled at his mind's seeming inability to move away from the issue of them leaving. He was like a kid with abandonment issues. He shook his head and laughed quietly.

Sheppard was right about one thing. Tomorrow was an important day. He would be completely useless if he was like this on the mission. It was time to admit defeat. There was no way he was going to figure it all out in one day. He had to go to his quarters and get some well-earned rest.

He saved his work and locked the tablets away so that no one else would either read them or use them and started to make his way to his room. He ignored the people he passed, unable and unwilling to give a simple greeting.

This time tomorrow, Doctor Elizabeth Weir would be back home. He was nervous about it, that much he could admit. Not just because he had the enormous responsibility of overseeing the bid to make her body but because this was his fault. He knew now that he should not have awoken the inert nanites in Elizabeth. She would have died if he hadn't, but he was pretty sure death was preferable to all she had been through. Would she forgive him? Would she trust him? At least if he was successful in building that body it would go some way to proving himself to her. She had been another of the few friends he had lost and he would do just about anything to get her back.

He wondered if she loved John. Elizabeth had been a master at keeping her feelings to herself, but he could tell that she trusted him and relied upon him more than anyone else in Atlantis. She would smile as his jokes, even when they were stupid (which was more often than not). She gave him so much more leeway than she gave anyone else. Not that he always got what he wanted, he still had to make a good argument.

That was when it hit him. At first glance, there were no two people more different than Elizabeth Weir, world-famous, peace-loving diplomat, and John Sheppard, infamous Air Force flyboy. But they worked with each other for three years to make the Atlantis Expedition a success and they had done it well. Together. That was probably why the kiss wasn't weird. In his subconscious, he supposed, he always thought they would end up together. They were like the Atlantis version of Carol and Mike in _The Brady Bunch_. They brought two disparate groups together – civilian and military – and made them one big family.

_Okay,_ he thought as he reached his quarters and opened the doors. _You just compared the Atlantis Expedition to _The Brady Bunch. He had officially lost his marbles.

It was late afternoon so it was light in the room and Jennifer was still at work. Suddenly feeling exhaustion weighing him down, Rodney all but dragged his body to his small bed and collapsed on it, not even thinking of changing his clothing. He passed out seconds later, his dreams filled with Elizabeth and John, in sixties clothing, both of them telling Lorne how he needed to be nice to Rodney, his new brother.

* * *

Lieutenant Colonel Evan Lorne stood on the highest balcony of the control tower overlooking the East Pier. It was dusk. The moons were slowly becoming visible, brightening the skies of Atlantis, before the darkness of night would soon take over.

His canvas on the easel was blank. He had been waiting for the moment that would be memorialised by his oil paints and he could see it forming before him now. New Lantea was beautiful. Atlantis was beautiful. He hoped that maybe one day he would be able to show his paintings to people who did not require security clearance.

Colonel Sheppard had come to see him several hours before to tell him that Woolsey had scheduled the rescue mission for Doctor Weir for tomorrow. Actually, he had called it Operation Sedgewick. When Lorne had chuckled, Sheppard looked confused so he explained that he liked the fact that he named the mission after Doctor Weir's dog. At that moment he could see that the Colonel wasn't happy that he knew that little fact, so he swiftly changed the subject, asking how he convinced Rodney to take part, given that he had seemed so against it last night. Sheppard stated it actually wasn't that difficult in the end. He then told Lorne to take the day and relax.

Relaxation had not been that easy. That morning he had looked out of his window, wondering about painting but knew he would not find inspiration until later in the day. When one had been painting as long as he had, one knew when inspiration struck and could also estimate when said inspiration would strike.

He spent the first part of the day wandering the halls of Atlantis. He went to the Mess Hall and chatted with some of the off-duty personnel there. He gathered some of the new members of the military contingent and watched as they each had their asses kicked by a rather wound-up Ronon. That was fun.

He spent lunchtime trying and failing to beat Zelenka at chess back in the Mess Hall. That was less fun. Zelenka told Evan that he was avoiding McKay who had been up all night working on something "top secret" which meant he was more insufferable than usual. Evan wondered if that was even possible.

After lunch, he went to the Armoury and prepared the weaponry that would be needed for tomorrow. He cleared an area in the corner of the room and placed four P-90s, four nine millimetre handguns and five fully charged Anti-Replicator Guns there, along with spare clips and crystals. He placed a note on top stating "DO NOT TOUCH, COLONEL LORNE". He had to cross out the 'M' as he started to write 'Major'. It had been two months since his promotion on Earth and he was still getting used to it. How long it would be before he was completely comfortable with it, he didn't know.

Leaving the Armoury, he followed the corridor into the nearby Gate Room. There was very little activity around the Stargate, no teams were off-world at present and the next scheduled mission was theirs. He looked up and around. Despite living here for more than four years now he was still over-awed by the scale and grandeur of Atlantis. Even this room was a wondrous sight. Certainly, the SGC under Cheyenne Mountain didn't even remotely compare.

His eyes remaining on the glass walls of Mr Woolsey's office, his mind went back to a time when the room overlooking the 'Gate was occupied by Doctor Elizabeth Weir. He had been wary when he first arrived in the Pegasus Galaxy. He had actually worked for her before when she had been in charge at Stargate Command for a short time. However, at that time 'Gate travel had been suspended due to the Government Review. Their interaction at that time had been fairly minimal.

That was wholly different from coming to a galaxy far, far away from Earth and joining a civilian/military expedition run by a civilian. Even one as capable as Doctor Weir. There was a very different atmosphere here. It was calmer than a full military base, it was more like a family. Everyone still worked as hard as they did at the SGC, but looked to each other for support.

It became clear to him quickly that Doctor Weir had worked to foster that kind of environment, closely assisted by Colonel Sheppard. They worked well together and weathered storm after storm. Elizabeth Weir was a good leader, one of the best he had worked under, in a career that included working for Generals Hammond and O'Neill. He had a great deal of respect and admiration for her… as well as something else he had never allowed himself to think about.

Evan was usually on the base when Sheppard and his team were off-world and in trouble. He saw how she worried about them, more so than when any other team was away. She would deny it but Lorne saw the anxiety before Sheppard came home and the relief when she laid eyes on him again. He wasn't oblivious and he was quite sure of what that meant, though he was never bold enough to ask. Not that it was any of his business anyway.

For his part, Sheppard kept his cards close to his chest. He had a bit of reputation as a ladies' man but Lorne had seen little actual evidence of this, not that he was really looking. Once Lorne became aware of Doctor Weir's feelings however, he made a point of watching his commanding officer when he was around her. The one thing he noticed outside of the frequent longer-than-necessary moments of eye contact was when Sheppard's team returned from a mission, he would look around the Gate Room until he found her. And she was usually on her way down the stairs from the Control Room.

After Weir was left on Asuras, Lorne had tried to talk to Sheppard about returning for her. Sheppard had said he had to come up with a plan. Plus, he needed to figure out a how to protect Atlantis from her. As time went on and no plan came to fruition, then the incident with her consciousness coming to Atlantis occurred, he watched his C.O fade away, become a shadow of himself. And that had been how he lived his life – until now.

He hoped that they were able to fully complete their mission. He hoped they would be able to get her into a body and somehow deal with all the fallout from Earth when they found out what they had done.

Of course, he was concerned as well. There was a possibility that Doctor Weir would be dangerous. He sincerely hoped not. If there was anyone who deserved another shot at life, it was her. She was an incredible woman, she really was.

Snapping back to reality, Evan looked at the canvas. He had been so deep in thought he didn't remember actually painting. He smiled. It wasn't quite what he planned, but sometimes, planning was overrated. A balcony under a navy blue sky, two moons peeking through the clouds. And on that balcony, a woman in a red shirt and grey trousers with long brown wavy hair, looking upwards.

It was good, even if he did say so himself. _Still, better to make sure Sheppard doesn't see it,_ he thought.

* * *

Ronon Dex hit the red punching bag with such force it broke from its chain and flew across the gymnasium.

He bent forwards, his hands on his knees, as he breathed heavily. He was not calm and could not find a way to reach anything resembling that state. He had gone for a run, shot all the weapons available in the firing range, trained with and beaten a few of the military contingent and finally decided on lone sparring. None of it worked. He rose, walked over to the bag and hung it up again.

He saw himself in the wall of mirrors to the left of the doors. He looked more tired than he felt. When Sheppard had come to see him he had been glad to hear that Woolsey had approved the operation. But to be told to take the day off? He wasn't a man who sat around and waited. He was a man of action, always had been. He didn't like waiting. He just wanted to get on with it.

Ronon had always believed this day would come. John Sheppard was never one to leave things unfinished and Doctor Weir was one hell of a loose end, particularly for him.

In all honesty, Ronon was still hesitant about whether the Replicator could be trusted. She had lied to them after all. But then she made a huge sacrifice. It had not been made known to her where she and the other Asurans would be sent, her reasoning being that she did not want to inadvertently let the others know, which was logical. However, Doctor Jackson had been right. There was no way Ronon would want to end up where she did. He would rather die than be left that way.

It had been obvious to him that Sheppard was not the same person after that incident. He never said anything because that wasn't the kind of people they were. He considered the Colonel one of his best friends, but even all this time, he had not told him about Melena, other than that he had lost her on Sateda. He never expected Sheppard to confide in him.

He looked outside at the skies above Atlantis. It was dark and the two visible moons shone brightly. It was very late and he needed to get some sleep.

Right now though, he knew that wasn't going to happen. He was too wired, unable to unwind. Nothing was wearing him out.

Nothing could stop him thinking about Weir and what would happen when they brought her back. Would McKay succeed in creating a new body for her? Would she be safe to be around? Would Sheppard be able to keep perspective when it came to her and what she was? Would it be down to Ronon himself to deal with her if Sheppard couldn't?

Without realising it, his right fist thrust out and drove into the tough hide of the punching bag. He looked at his arm to the point where his hand was entirely inside the bag. _Damn._ With some effort, he pulled his hand out and flexed his fingers. They hurt a little but no more than that.

He walked towards the doors and exited the gym, certain he would not find peace here. He went to the transporter and beamed to the living quarters.

He did want to help Weir if it was possible. He owed her everything. She gave him a home at a time when he had been without one for seven years, a family when he had lost his and a way to take his vengeance on the Wraith who had made him suffer all that time. Sheppard may have found him but Doctor Weir was the one who allowed him to stay.

Realising he was thinking about the situation again, he recognised that sleep was not going to come easily. But there was still one option left open to him. He stopped outside the room and chimed. It took about a minute but the doors parted to reveal a tall, very attractive, woman with her brown hair loose around her shoulders, wearing matching blue tank top and shorts. Ronon took in her appearance, stunned that a woman like this could be interested in a guy as simple as him. She was strong and funny and complicated. He was… strong.

Amelia smiled sleepily at him. "Are you all right, Ronon?"

Ronon wanted to lie, to tell her he was fine. But he found he could not. He _wanted_ to be honest with her. He couldn't tell her about the mission but he could still talk to her. "No," he finally answered. "Can't sleep."

"Wanna come in?" She stood to the side to allow him room to enter.

He nodded and moved inside. The doors closed behind them. Amelia walked past him to the bed and sat on it. Ronon slowly lowered himself onto the bed beside her. She said nothing.

After some minutes, she spoke. "You should lie down. You need to rest before you go tomorrow."

Ronon silently agreed and lay down on the single sized bed. Amelia shifted as he positioned himself, resting her head and hand on his chest.

Ronon felt his heartbeat slow as he listened to his girlfriend's breathing even out. Maybe he had gone about today all wrong. Instead of relaxing and enjoying himself he spent the time brooding over his various worries about the mission. But now, although the fears were still there, the mere presence of Amelia gave him some peace of mind. They didn't actually get a chance to talk but it seemed that wasn't what he needed.

Kissing her on the top of her head, he whispered his thanks as he drifted to sleep.

* * *

John Sheppard couldn't sleep. Lying in his bed in a black T-shirt and boxers, he drummed his fingers on his chest whilst staring up at the ceiling. The room was dark but the moons' rays gently brightened it.

His day off had consisted of him getting Puddle Jumper One ready for the mission, wandering aimlessly around the still abandoned rooms of the North Pier tower and wishing the day would just be over already so he could get going.

Believing that the incredibly long walkabout had tired him out sufficiently, he returned to his quarters and got ready for bed at 21:00 hours – early for him. And now, here he was, five hours later, not sleeping.

It wasn't for lack of trying. Every time he closed his eyes, he saw Elizabeth. In her original form, floating in space. Her skin was blue, her eyes closed. The last time he tried to sleep, he saw the same vision but this time her eyes slowly opened. She said nothing but the accusatory glare was enough to put him off for a while.

It took him a moment to realise he was humming. It was the same song. He just couldn't get it out of his head. He had been asked by Rodney why he had been whistling that song. Of course, Rodney had been his usual sarcastic self about it and John diverted him away from the subject.

However, the lyrics had been in his head for some time now. It was only now he decided to truly analyse it. Why not? It wasn't like he was going to sleep.

He thought back to the Infirmary at Stargate Command three years before. He had led one of the SG teams for six weeks when the Expedition had been unceremoniously kicked out of Atlantis by a group of returning Ancients. Three weeks into the stint, he was sitting on a bed in the Infirmary awaiting a post-mission examination. The curtain was drawn around the bed as the rest of his team were having their own check-ups. Someone had decided to play some music and _Woman_ came on. With nothing else to do, John laid his head on the pillow, hands behind his head, and idly listened.

_And, woman, I will try to express, _

_My inner feelings and thankfulness,_

_For showing me the meaning of success _

It was at those words that John pictured Elizabeth. She was on the balcony outside the Control Room and she was smiling. He sat up quickly, paying more attention to the song as it continued. Each word Lennon uttered reminded him of his former boss and of feelings he had been trying to ignore for over a year, particularly since she had kissed him whilst they were under the influence of Phoebus and Thalen.

In that moment, sitting in privacy in the Infirmary, he realised that the reasons he had kept his feelings to himself (disapproval of the IOA and the SGC, splitting focus, a possible relationship being used against them or the Expedition, undermining of their leadership) were no longer applicable. He loved her and he wasn't going to hide it anymore. He resolved that he was going to ask her on a date – if he was ever able to talk to her.

The next time he had seen her was three weeks later when she had joined himself, McKay and Beckett for dinner. Her presence was a surprise, a pleasant one and he hastily decided that he would escort her home and when he was alone with her he would ask. He was terrified, but determined.

However, fate had intervened. Dinner ended with a summons to the SGC and they were informed by General Landry that the Replicators had attacked Atlantis and killed the Ancients. Events unfolded as they had, and soon they were home and life resumed as it had before. It wasn't that he was unhappy that they were back but he was disappointed. He never even got the chance to gauge her feelings for him. He buried his affection for her again, along with the song, and carried on as normal.

He never allowed the song to enter his thoughts again. Thankfully, living on a military base in another galaxy meant that he didn't really have to hear it either.

It was as he was driving back to the SGC from Dave's house that he turned on the car stereo. As if to strengthen his determination _Woman_ started almost straightaway. And it had not gone away since. It played in the back of his mind constantly, a background theme to everything he thought, said and did. Not that it bothered him. Any other song would probably have driven him mad. This song gave him strength, faith. As long as the song was playing, he could believe that this was going to work, that he was going to get Elizabeth back.

John closed his eyes again and just listened to the words. This time, the image of Elizabeth he saw was one of her on the balcony, wearing her regulation clothing and smiling as she looked up at him. Her green eyes sparkled with happiness. He didn't even notice he had fallen asleep.

* * *

As Sheppard approached the Jumper Bay he caught himself whistling again.

This was a huge day. Today, he would finally and gladly say goodbye to the Replicators one last time and take back what they stole from him, what they stole from them all. He was looking forward to it and had to keep himself from running.

John entered Puddle Jumper One and was pleased to see four expectant heads turn to him. And he thought _he _was early. Rodney, Teyla, Ronon and Lorne were all such good and loyal friends to both himself and Elizabeth. This mission was voluntary, given the risk involved, yet they were all here. For these people it was never a matter of volunteering – if it meant helping Elizabeth, there was no choice. As it was for him. They loved her, not in the same way as him, but they did.

Starting to feel slightly uncomfortable with the direction of his thoughts, he smiled weakly and made his way to the pilot's chair. He swiftly went through the pre-flight protocols and activated the radio. "Control Room, Jumper One is ready to depart."

"Very well, Jumper One," Woolsey's voice responded. "You have a go."

"Thank you, Sir." John nodded to Rodney to his right, who dialled their destination into the DHD.

The Heads-Up Display informed him when the Stargate was active and John smoothly lifted off the bay floor and lowered the puddle jumper down into the Gate Room. He saw Woolsey standing on the balcony overlooking the Stargate. John turned the jumper until they were facing the beautifully shimmering event horizon.

"Good luck, Colonel," he heard Woolsey say.

John closed his eyes for a moment. This was it. Just a quick trip through the wormhole and he would be reunited with the woman he loved. The butterflies in his stomach were fluttering heavily and his nerves were starting to fray. The same pessimistic questions started to invade: would she be all right? Would she hate him for abandoning her for so long? Would she be angry at him for coming for her?

He pushed it all away. Opening his eyes again, he moved the jumper forward and through the Stargate.

He pulled the jumper to a stop as soon as they exited the Space Gate. The HUD automatically displayed a diagram of the area before them. Red blinking dots indicated that the Asurans were straight ahead.

"Oh, no."

John turned to Rodney beside him. "What is it?" he asked, as he noticed the look of horror. His stomach felt like it was sinking.

McKay pointed to the display but seemed unable to speak. That could not be good.

There was a sharp intake of breath and John looked up to see that Teyla was standing between himself and Rodney in the front seats, staring at the HUD. "There are only seven lights."

John swung his head back. Counting the lights three times, he could only swallow as he saw Teyla was right. Seven lights, seven signals. There should have been eight. One body was missing. Where was it? Who was it?

He was frozen in his chair. Movement was impossible. What if it was her? What if she was gone? That old familiar pain in his chest started to bloom, as if it had not died when the mission was authorised, but had hidden itself, waiting for his soul to be crushed to reappear and mock his temporary elation. As the pain swelled, John noticed Lennon's words fade until the song died away altogether.

He wasn't sure he would be able to deal with this. If she was gone, if he couldn't save her, if he had let her down again… He took his hands off the control panel, feeling them begin to tremble. He thought he could hear his name being called from very far away. For a moment, it sounded like Elizabeth's voice.

"John!" The female voice was closer now and it wasn't Elizabeth. He glanced to his right, finding Teyla crouched beside him, fear and concern etched on her face. Her expression was enough to snap him out of his stupor.

"Are you all right?" she asked softly.

John turned away from her searching eyes and gulped, doing his best to keep his voice from breaking. "We need to get closer."

He heard Rodney speak up to agree but did not look over. He kept his eyes glued straight ahead. He couldn't let anyone see, especially Teyla and Rodney. He was having trouble covering his emotions this time, his mind seemingly refusing to let the usual walls come up. He couldn't let them see.

Pushing all his concentration to piloting the jumper, they started moving slowly forward. It was only moments before the bodies were right in front of them. They were blurred as he kept his focus on the jumper display. But he had to look.

Colonel John Sheppard called on all his military training and experience to help him find some strength. He could do this, he needed to do this. Taking a deep breath, he refocused towards the front windscreen. He could see the bodies. The HUD then assisted by showing him close-ups of each of their faces – four females and three males.

The last tendril of hope within his heart dwindled away. His mind felt empty with the absence of their song. However, he could do nothing but face the devastating truth.

Elizabeth was the missing Replicator. He was too late.

* * *

**Further A/N:** I don't normally put any notes after a chapter but I just wanted to say with regards to the song. I don't normally write songfics but this is a song that I do associate with Sparky. If you have never heard it before I implore you all to listen to it, it's amazing - as is a lot of his work. If you have heard it before, listen to it with Sheppard in mind. Maybe it's just me.


	12. Chapter 12

**Chapter 12**

Teyla studied her friend carefully. He appeared to be in a state of catatonia, his stare fixed on the HUD, his body not making any movement at all. His face made her heart break, his mouth closed tight and his eyes glistening.

Still crouching beside him, she heard Rodney ask, his voice shaky, "Is he okay?"

Teyla turned to him. She saw fear and a great sadness in his blue eyes and immediately understood. John had told him. At Rodney's slight nod, she realised that he could see he was not alone with that knowledge.

She returned her attention to Sheppard and placed a hand on his arm. He did not flinch. She could sense Ronon and Evan had moved closer to the front seats but they said nothing.

She shook his arm gently. "John?" she spoke softly.

No response.

She shook harder. "Colonel Sheppard!" she said in her most authoritative tone.

That worked. John blinked twice, then turned around to look at them all. His tears were unshed but the sorrow she saw made her lower her own head so he would not see her own tears forming. How could they have come this far only to lose her in this fashion? How could he continue without knowing what happened to her? After regaining control, she raised her head again.

"Rodney." John's voice was quiet and on the verge of cracking. "Can you tell what happened?"

Rodney was tapping away furiously on his tablet, his attention constantly shifting from the screen to the jumper's display. He was obviously avoiding facing John. He sighed heavily. "No."

Rodney suddenly stood up. He looked at Lorne and Ronon. "Go grab the ARGs!" he ordered.

"What're you thinking?" asked Lorne, as Ronon headed through the doorway to the rear compartment.

Teyla stood from her position and turned to McKay, moving herself to behind John's chair so he could see the scientist as well.

"We ask," said Rodney, in response to Lorne.

"Who?" asked Ronon as he re-entered with two ARGs, which he handed to Lorne and Teyla.

Rodney pointed to the front windscreen and HUD. "Them."

Silence greeted his revelation. "Look," he said, immediately frustrated. "It's pretty obvious. We bring one of the Replicators on board, we just scoop it into the back of the jumper, like we did with Niam. Then we revive it and ask it about…" He swallowed. "About Elizabeth."

"Is that wise?" asked Teyla, very aware that, apart from the original question to McKay, John had yet to contribute to the discussion. "When you revived Niam, he attacked you."

Rodney pointed to the weapon in her hands. "Which is we'll have those."

Ronon returned to the rear and brought back three more ARGs.

John rose and took the proffered gun. Teyla looked at him and he nodded. He had pulled himself together. "Do you really think they'll know anything? They've been Replicator popsicles for the last six months." His words were light but his voice was thick with emotion.

"They still have the subspace link, at least with each other. Maybe they know what happened to her, maybe someone took her and they know where she is," Rodney said, studying his ARG with great interest.

"Okay," said John, his voice returning to his usual more business-like tone. Having a course of action was spurring him on. "Let's do this." He sat back down in the pilot's chair and looked carefully at the signals on the HUD. He pointed to the one to the left of the display, on the outer edge of the group. "That one," he said, resolutely.

Rodney went to the doors to the rear compartment and shut them using the control panel to the right. All the men took their seats while Teyla remained standing between John and Rodney at the front. Taking one final glance at John, she could see that he had closed himself off. His response earlier was atypical, which told her how much of himself he had put into this mission. Now, he had a new goal and he was clinging to it. Hopefully, the Asuran they retrieved would be able to give them some positive news. She was unsure how John would react if she was lost to him. She did not know how she would be able to help him, if he could even be helped.

* * *

John pushed all his concentration into the positioning of Puddle Jumper One's rear hatch to collect the Asuran he had targeted. It was on the outside of the group, so he hoped it would be the easiest to scoop up. The doors between the cockpit and the rear were sealed, so he was relying on the HUD to communicate to him when it was on board.

As he guided the jumper backwards, he tried not to notice the deafening silence in his head. One of these Asurans had to know something. He just didn't know what he wanted to hear. Not that she had been destroyed. That she had been taken? That did not bode well for Elizabeth if it was the case. In fact, knowing her as he did, she would rather destruction over imprisonment, possibly to be used against Atlantis.

He started repeating a mantra in his mind, in an attempt to give himself hope and fill the void: _I'll find you Elizabeth. I'll find you Elizabeth._

The Heads Up Display as well as his mind's connection with the jumper told him that the chosen body was now within the rear compartment. He hit the button on the dashboard to shut the rear hatch.

Time passed slowly as they sat waiting for the hatch to fully close. The mantra kept replaying itself. He dared not look at the others, particularly Teyla and Rodney. His behaviour of a few minutes ago could not happen again. If he saw pity from either one of them it would push him over the edge and he doubted he had the strength to pull himself back up. But he knew he had to find it from somewhere. He still had to destroy the remaining Replicators and bring his team home. He could fall apart when he was back in his quarters and everyone was safe.

He was brought out of his dark thoughts by a beeping sound.

"Rear compartment is sealed and re-pressurised," announced Rodney in a neutral tone.

They all stood at once but remained in place, allowing John to step out and lead the way. He reached the double doors and went to the panel. His hand hovered over the switch. Taking a deep breath he activated the switch and the doors slid apart.

He immediately readied himself to fire his ARG. On the floor between the benches along each side of the rear compartment laid a male body. Wearing the standard off-white trousers and shirt, the Replicator was facing the ceiling. It was Caucasian, obviously tall and muscular with short blond hair. It's most distinctive feature, though, was the hook nose. John vaguely remembered seeing it on Atlantis. However, its skin was covered with ice and its eyes were closed. One hand was stretched up towards the ceiling, unmoving. It was completely frozen.

John moved forward slowly. The feet were facing towards the cockpit. John tapped one with his own foot. He could feel the solidity, even through his steel toe-capped boot. "Rodney?" he said, his voice barely above a whisper.

McKay moved to into the compartment to stand beside him, tablet in his grip. He looked from the Replicator to his screen. "Give me a minute to hack into his systems." He tapped the tablet several times. "Okay, he's not active."

John's arms dropped down with the ARG. "I think I got that already," he drawled, irritably. "How long to revive him?"

"Well, when I revived Niam I increased the activity of his nanites incrementally. When I sped up the process his … awakening, I suppose, was almost instantaneous.

"Do it then," commanded Sheppard.

"Hold on," said Rodney. "I have no idea what could happen if I start him at full power. He could blow up or he could go nuts on us."

Sheppard raised the ARG again. "That's why we have these." He started moving around the frozen body to the right and positioned himself by the Replicator's head to the side of the rear hatch. "Let's cover it on all sides, guys, but away from the rear hatch, in case we need to use it."

Lorne stepped into the compartment and down the left side. John put his hand up when he was halfway. Lorne stopped. Teyla then took up the same position on the opposite side, a short distance from John. Ronon stayed at the Replicator's feet next to Rodney who stared at it, eyes wide with fear.

When everyone but McKay had their weapons trained on the body, John bowed his head. "Do it."

"Okay." Rodney's voice quivered. "I'm doing it faster than last time but not too fast. It should only take a few minutes."

John kept his eyes on the target, listening to the sounds the tablet made as the scientist entered his commands. Keeping his concentration on the Replicator, John waited and waited, knowing that any lapse in concentration could lead to someone on his team being injured or killed. That was what got the whole mess started in the first place. If he had been concentrating on Elizabeth more when they first escaped Asuras with Niam in tow, maybe he would have been able to stop Niam putting his hands around her throat, infecting her with nanites. He did the best he could, pushing him off of her and into the rear of the jumper. His best wasn't good enough. It was done. Now, they were here, he was waiting, wishing to know what had become of his friend, of the woman –

"His nanite activity is rising," Rodney called out. "Get ready!"

The Replicator's eyes flipped open and it sat up, it's back rod straight. John kept his ARG on it, anticipating any threatening movements.

The Replicator looked around at its captors. When it saw Sheppard, it seemed to recognise the situation in which it had awoken. It slowly got to its feet and turned to face Sheppard. Its face twisted into and expression of anger, an odd thing to see, given that was still covered in ice. It was disconcerting. Its arm rose towards him and it pointed. "You," he spat.

Sheppard took a step forward, still pointing his gun at it. "Okay," he said calmly. "No sudden movements, we just wanna talk."

"You lied to us," said the Replicator softly, but with a bitter edge. "She lied to us."

"Yes, she did." John kept his voice the same. "She was protecting us. You were a threat to Atlantis."

"Koracen was acting alone and Doctor Weir killed him," said the Replicator. "She asked us to trust you and we did. She betrayed us."

"Look, I know you're upset –"

The Replicator laughed – sarcastically? "Upset?" it said. "That does not even begin to scratch the surface."

John's patience was running out. He was a soldier, not a therapist. He didn't have time to deal with the hurt feelings of a machine. However, before he could say it aloud, Teyla took control, shifting to stand next to Sheppard.

"I understand that what we did has made you angry," she started, in that soothing way that had been able to prevent rants from Rodney, violence from Ronon and recklessness from John and to lull her child into slumber. "But you must also understand the danger you posed to us. You threatened us, blackmailed us and one of your people turned against us after we agreed to help you. Elizabeth felt there was no other choice."

The Asuran seemed to be processing Teyla's words. Its shoulders dropped, though not by a lot as it appeared to be stiff. "She may have been right. Some of the others were unhappy with the way we were being treated and did not trust Doctor Weir's reasons for killing Koracen."

Seeing its resignation, John slightly lowered his ARG. What's your name?" he asked, trying to show a bit more kindness than he had before. But it was difficult. As far as he was concerned, this thing was one of the bastards that had taken their leader away and changed her into what she later became. However, if he wanted its help, displaying his hatred and mistrust was unlikely to make the Replicator more inclined to give it.

"Ando," it replied. "What do you want with me?"

Teyla answered. "We are in need of your assistance."

Ando sighed. "What is it you require?"

Rodney sputtered slightly. "What, and you'll help us, just like that?" he exclaimed, disbelievingly.

Ando turned its body in Ronon and Rodney's direction. Ronon tensed, prepared to fire. "I do not know what it is you need from me unless you tell me. Then I shall decide if I will help you."

"Oh," said Rodney, as if that made more sense to him.

John cleared his throat in an attempt to get the Replicator's attention back to himself and Teyla. "That's great, thanks." Now the Replicator – Ando – was facing him, he dove in. "We came here to find Doctor Weir, but she seems to be gone. You don't happen to know where she is, do you?"

"No."

There it was. He had pretty much expected that very answer, but part of him had hoped that what Ando told them would give him the possibility that she was still out there somewhere. Somewhere he could find her. He could see past Ando to the devastation on McKay's face as well and suspected his own expression held something similar.

Ando continued. "You are Colonel Sheppard, are you not?"

John heard the question and, unable to trust his own voice, nodded once.

"Before we came to Atlantis, she had given up hope of seeing you again."

John said nothing.

"Doctor Weir was afraid you would think less of her."

John could hear the cracks as he answered, "I never did."

"Really?" Ando clearly did not believe him.

Recalling the words he had spoken to Elizabeth when he chased her and Koracen, John swallowed, the guilt causing his throat to catch. Swallowing again, he tried to speak. "I wasn't sure it was her, not until she took you through the Stargate." He hoped his honesty would make Ando understand.

Ando sighed again. It made him – it – seem so human. The frost on its skin and clothing was starting to melt within the warmth of the jumper. "After she led us here, she cut herself off from us."

"What do you mean?" questioned Teyla.

"As you are no doubt aware, we are connected to each other through a subspace link. This allowed us to continue to communicate with each other, even though all our other functions essentially frozen," Ando explained. "At first, all anyone communicated was their… displeasure to Doctor Weir."

"That is understandable," said Teyla. John disagreed but didn't say anything. To him, they deserved it. Not Elizabeth, just them.

"Doctor Weir said she was sorry, but she couldn't risk the safety of _her_ people. Then she cut herself off. We were never able to communicate with her again."

John couldn't help the wry smile as his heart swelled with pride at her final act of loyalty. If only he could tell her that…

"Despite this, we were always able to sense her presence," Ando stated. "Until recently, that is."

"What happened?" asked John.

"She vanished – or at least her presence in the link did."

"When?" demanded John.

"77,760 of your minutes ago."

"That's more than seven weeks ago," Rodney said.

"Fifty-four days," clarified John, without having to think. He was always good with numbers.

"I know that," moaned Rodney.

"And you do not know why she disappeared from your link?" asked Teyla.

"I do not."

"Thank you."

"You could scan the region for traces of neutronium. If there is none it could indicate that she was not destroyed but removed," Ando suggested.

Rodney opened his mouth, ready to protest. "It's possible some traces may have been caught in the orbit of the Space Gate's planet," he said, more to himself than anyone else. "Give me a minute." He walked out to the cockpit and John caught glimpses of him connecting his computer tablet under the dashboard. "I'm increasing the sensitivity of the jumper's sensors and redirecting them," he called back. "All right, here we…"

John saw Rodney collapse into the co-pilot's chair. John stopped breathing, waiting for him to tell them what he had found. But, given his posture in the chair, there was little doubt what the news would be.

After a moment, McKay got up and trudged back to the rear compartment, leaning on the doorframe as if he could barely carry himself forward.

Lorne spoke up. "What did you see?"

"There were traces of neutronium orbiting the planet. The rest of it, I guess, had seven weeks to… float away," McKay croaked.

John let go of the breath he was holding and stepped back as if physically hit by the information. His legs felt weak and he wanted to drop to the floor, to allow them to rest from keeping his body up – a body that felt so heavy, yet empty at the same time. There was nothing left. Nothing within, nothing without. He started to sink, despair taking over, but saw Rodney and Ronon behind the Replicator.

He stopped himself from falling, realising he still had more to do. He looked to Ando and, with as much self-control as he could muster, said, "Thank you."

Ando merely nodded. "May I ask you a question, Colonel?"

"Sure," John rasped, absently.

"Are you planning to kill us?"

His voice was so matter-of-fact as he asked the question, John looked to the floor, apprehension hitting him suddenly. This Replicator had been very helpful and seemed to understand their position. He had to be truthful. "Yes."

"I see." Ando went quiet, as if contemplating something. "I would appreciate it if you would not awaken the others."

"You're okay with this?" asked Ronon.

"Death is better than the way in which we suffer now."

Ronon bowed his head slightly, seemingly comprehending Ando's response. He never took his eyes from him, though.

As John raised his ARG again, Ando spoke. "Would it be possible for you to destroy the others in one go? That way, they will not know anything from our link beyond my own loss."

John considered his request. Elizabeth would have thought it reasonable. "Rodney?"

"Huh? What?" McKay came out of his stupor as he heard his name.

"Can we connect the crystal from an ARG to the jumper's cloak and use it to get all of them at once? Like we did on Asuras?" he prompted.

"We had a ZedPM when we did that," replied Rodney, looking down.

"Yeah, but we're only targeting one area for a very short time," argued John, unable to shout.

"Um… give me a sec," Rodney went over to the left side of the compartment and pulled the panel from the wall above the bench. John watched as he pulled various crystals out and switched them around. He found if he focused on what was going on around him he was able to keep himself from drifting to other things.

Eventually, Rodney removed the crystal from his ARG and placed it in a slot in the panel he had left empty. "That should do it," he pronounced quietly.

John returned his attention to Ando.

"Thank you," the Replicator said.

John gave a short nod and took a deep breath. Firing his weapon, he was amazed at how quickly the body before him broke down into a pile of tiny grey blocks on the floor. The pieces were no longer a threat, the bonds between them permanently broken. The ARG dropped out of his hands and clattered to the metal floor. Rodney jumped at the sound. Everyone looked at him, their shock plain to see.

"Let's get this done," he said as he passed them and went into the cockpit. His body felt as if it was on autopilot, doing what it needed to do without his brain telling it. He sat in his chair as the others joined him, and looked out of the viewport to the remaining bodies.

"I converted the cloak to the shield. All you have to do is activate it and spread it to envelope the Replicators. The shield will do the rest," Rodney instructed.

With all the concentration he could gather, John's mind activated the shield. Once again gazing through the window, he pushed outwards and watched as the shield made contact with each Replicator and broke them apart, one after the other. Soon, there was nothing more than a dust cloud of useless neutronium blocks.

"I guess that's it," Lorne said, sadly.

"Yeah," was all John could get out. He deactivated the shield and, taking control of the jumper, turned the vessel back towards the floating Stargate. As the jumper moved forward, Rodney dialled the 'Gate. They watched as the pool shot out and settled. John fixated only on getting the people he had with him home, not allowing himself to break. He couldn't break, not yet.

* * *

After their post-mission medical check-ups, Woolsey had insisted on a debriefing in the conference room. Rodney felt it was completely ridiculous. It was obvious on their return that the mission hadn't gone as planned. Could Woolsey leave them alone to wallow, just for a little while?

Woolsey sat at the head of his grand mahogany table, Ronon and Teyla situated to his left and Rodney and Lorne to his right. John sat at the opposite end from Woolsey.

John remained silent, staring at the unblemished surface of the table, whilst Rodney, Lorne and Teyla took turns as they explained what happened.

When they were finished, Woolsey exhaled heavily and removed his glasses. He looked at each of them, seeing only miserable faces as far as Rodney could tell. His gaze rested on Sheppard at the end of the table, separate from the rest of them. "I am very sorry, Colonel."

John barely nodded. "Thank you," he said, monotonously.

"Well…" Woolsey said, awkwardly, "if that's all…"

They all watched as Sheppard leapt from his chair and power walked out of the room, without so much as a goodbye.

The others slowly followed, until Rodney was alone. He still couldn't believe it was over. John had managed to convince him that they were really going to get Elizabeth back this time and for good.

Now that it was done, he didn't know what to do. He felt drained, like he could pass out and not wake up for six months. He was utterly depressed and didn't feel like he could even get up at this point.

Elizabeth Weir had been his friend. She was a good person and a great boss, probably the best one he had ever worked for. Somehow, she always managed to keep his ego from growing exponentially, despite the frequency of his life-saving, ingenious plans. But, more than that, she made him feel like he was a good person and that she considered him a good friend. She treated him like a person and not an annoyance that had to be put up with, like other people had in the past.

He really only activated the nanites when she had been fatally injured because he didn't want to lose her. But losing her then might have been better than this. Elizabeth had been through hell in the last few years and for it to end this way seemed… wrong.

Poor Sheppard. If this was how he felt, he could only imagine what John was going through. His momentary loss of control on the jumper was something he had never seen before in the five-and-a-half years he had known him. It had only been for a minute or two but it had seemed like longer. John Sheppard was the strongest person he had ever met. He had never seen him broken, not until that moment.

And he didn't know which was worse: that Elizabeth had been mysteriously destroyed by an unknown party or that John would never know whether she felt the same.

It was beyond him. Not that he had lost a good friend, although that was hard to take. It was how she was lost. The argument that she could be taken by someone for her technology or the location of Earth was a viable one, but it was a very unlikely scenario. The system the Stargate inhabited was deserted. The Pegasus Galaxy was a huge place. The possibility that someone happened to come across eight stranded Replicators was incredibly remote. Not impossible, but it would seem more likely that their location was known.

However, for only one of those Replicators to be destroyed who just happened to be the one they were looking for – no. That was not a coincidence. Who did this? How did they find her? Why did they murder a good woman?

He needed to know. He would look into it, investigate, solve it. He would give Sheppard a purpose. He would find those who killed the woman his friend loved and paint a target on them.

He got up, feeling more invigorated, and walked to the doors, which opened for him as he approached. As he stalked down the stairs into the Control Room he saw Jennifer Keller standing at the railing overlooking the Gate Room, staring at him worriedly. She had carried out the check-ups on Sheppard and Teyla and could tell something was wrong. A single-celled organism would have been able to tell. She had told Rodney she would meet him after the debriefing. She had been waiting out here for him, he realised.

Rodney still didn't understand how he managed to get involved with Jennifer. She was blonde, beautiful, sweet and really smart. She was also completely sane. He was pretty sure that there were some people who did not think she could be if she was dating him, but who cared? She loved him and she got him. No one got him like she did.

Jennifer smiled softly at him and reached for his hand. "You wanna talk about it?"

He took the hand she offered him and pulled her into his arms for a much needed hug. "Let's go to my room. I'll tell you there." Revenge could wait until tomorrow, he decided. Right now he needed to be comforted.

As they walked to the transporter, hand in hand, Rodney's thoughts wandered back to John. He was sorry he couldn't see his two friends share what he now shared with Jennifer. He would give him some time alone for now, but maybe it would be a good idea to check on him later. He was pretty sure Teyla knew about John's feelings so resolved that she should come along too. Just in case he got all emotional.

Rodney wasn't good with emotional people.

* * *

John leaned back against the doors of his quarters as soon as they were closed. He shut his eyes tightly, trying to keep the tears from escaping. But they rolled down his cheeks anyway.

Crying was not something he did often. In fact, he couldn't remember the last time he did. So much had gone wrong since he came to Atlantis and each time he had refused to cry. However, he couldn't stop it today.

Elizabeth was dead. There was no way he could save her now. He would never know if she loved him back. He would never have a future with her.

A future. He snorted. There was no future for him. Elizabeth was his chance and she was gone. He didn't even want to think about tomorrow, let alone any sort of future that didn't include her.

He had truly believed he would find her. That she would be able to stay on Atlantis. He had pictured so many times finding her out on their balcony.

_He walked to the railings and stood to her right, as he always did. He turned and gazed at her as she watched the ocean._

_"__I missed this."_

_He reached over and took her hand. "I missed you," he replied._

_She looked down at their joined hands and then locked her emerald green eyes on his._

_"__I love you," he declared, unable to resist the earnest look she was giving him._

_She smiled, giggled slightly and looked down again. When her eyes came back up, they were shining brightly and John's mind went into overdrive. Maybe she was going to say it back._

_"__I love you too," she whispered._

John slid down the doors onto the floor, his elbows resting on his raised knees. His hands covered his face as he finally stopped trying to resist and let his grief take hold.

As he cried, he felt an overwhelming surge of anger. He rose to his feet and turned to the doors. With no consideration, except for the possibility of some kind of release, he clenched his fist and punched the right door. Nothing. It didn't even hurt. He hit it over and over again, until he saw blood spattered and smeared across the surface in and around the dents he had created.

Looking down at his hand, he could see his knuckles and fingers were completely red. This needed to be taken care of. Funny, it still didn't hurt, even though it obviously should have.

Slowly, he drifted to his bedside table and saw there was no tissue on it. He picked up a white T-shirt from the floor nearby and put it over the back of his hand. He watched as the blood quickly seeped through the thin material. He let it drop onto the bed.

He turned on the spot. How he hated this place. This room, this city, this planet, this galaxy. He hated it all, nothing good had come from him being here. He should never have come. He was an idiot for believing he could possibly do anything good here.

He picked up his guitar from its stand. Why did he bring this? He hadn't played it for years and wasn't even sure he could remember how. It was useless, pointless, a waste of space. Taking the instrument fully, he threw it across the room, hitting the opposite wall.

The surfboard went next. What had made him think to bring this? It landed next to the mangled guitar, still in one piece, but a chunk seemed to have come out of the wall.

The display unit by the windows crashed down as he pulled it over. Books and other objects flew from the shelves. He noted _War and Peace_ lying amongst the mess and felt another bout of rage burst forth.

He picked up the metal frame of the single bed and flipped it over, yelling incomprehensibly.

He ripped the Johnny Cash poster from the wall behind the bed and tore it in half. As the pieces dropped to the floor, he saw a small red crate that had been hidden under his bed – until he had removed it.

Falling heavily to his knees, he pulled open the lid with trepidation. He took out the first thing that caught his eye. A brown clay-type urn, the one he had given to Elizabeth on her first birthday in Atlantis. It had been such a surreal day, starting with him giving her the gift, then finding her elder self who had given her life to allow the Expedition to come to Atlantis and survive. The day ended with her death. He should have realised then how far she was prepared to go for her people.

The tears started to fall again and he had to control the urge to smash the pot. Instead, he carefully placed it on the floor beside the box. He pulled out each item one by one. A picture of Elizabeth standing proudly with his team. It was taken during the first month in Atlantis. The photograph included Aiden Ford. They all looked so serious but every one of them had a glint of anticipation in their eyes. John himself stood next to Elizabeth. He looked so young.

Next were a couple of articles of clothing. Her grey and red Atlantis uniform jacket. A red short sleeved top with a U-shaped cut in the chest area.

As he unfolded the shirt, something silver dropped into his lap. He put the shirt down and picked up the item.

It was an old-fashioned pocket watch with a long silver chain. It was her most treasured possession. Her father had given it to her before he died. He had seen her with it so many times, it was a comfort, her support. It meant everything to her.

He didn't mean to keep it from her mother. At the time the he had packed up her belongings, he had decided to keep only the pot and the picture. But he just couldn't bring himself to put it in the box going back to Earth on the Daedalus. He hadn't even realised until he had gone to his quarters for the night that he had put it in his shirt pocket.

_He was sitting in a clean and inhumanly tidy living room on a cream sofa decorated with blue flowers. He kept his head down, scratching the ear of the large white dog that had taken up residence at his feet, as the woman in the armchair to his right poured tea from an obviously fine china teapot into a matching fine china cup and pushed it towards him on the coffee table. He added milk and two cubes of sugar._

_"__Elizabeth mentioned you many times in her letters," Mrs Weir finally said, breaking the silence. "You seemed to be close."_

_"__We were," John answered truthfully. "She was one of my best friends… She believed in me at a time when no one else did." He bowed his head again._

_"__Elizabeth always saw the potential in people," said Mrs Weir, wistfully. "When it came to people, she had good instincts. It was one of the reasons she was so successful in her career."_

_John shrugged, not able to look in his friend's mother's eyes, afraid she would see that her daughter had been wrong this time._

_He did look up though, when Mrs Weir gently placed her hand on his knee. "Elizabeth was never wrong. If she saw something in you, then it is there. Even if you can't see it."_

_He was at a loss for words. This woman was so much like her daughter that it took effort not to shake her off and leave. That was what he did when things became too intense. He walked out._

_Instead, he smiled and nodded his thanks. She gave his knee a tap and then took her hand away._

_After another awkward period in which neither of them spoke, she was the one to break it again. "Was it you who sent my daughter's belongings?"_

_John cleared his throat. "It was."_

_"__I don't mean to sound rude but it seems that something is missing."_

_"__Really?" He tried to sound even._

_"__Yes," Mrs Weir replied. "It wasn't in her apartment but I didn't think she would leave without it anyway." John stayed quiet. "It was a silver pocket watch. It belonged to her father."_

_"__I saw Elizabeth holding it in her office a few times," John told her. "It was obvious it was important to her."_

_"__You didn't see it when you were packing her things?"_

_John paused, about to confess, then said unexpectedly, "No."_

_"__Oh," she said, disappointed._

_Feeling remorseful, John leaned toward her. "When I get back, I'll have another look in her quarters. Maybe she hid it somewhere to keep it safe."_

_"__Thank you, Colonel."_

_"__Call me John," he said. "All my friends do."_

_He left half an hour later, having to work hard to get out of staying for dinner. Back at the hotel, he threw off his blue Air Force blazer and hat. Reaching into his trouser pocket, he pulled out the watch. _

_"__Next time," he said aloud to no one, "I'll give it back next time."_

Holding the precious item in his hand, John closed his hand around it. His body felt weak, like it would break apart if he stayed upright any longer, so he laid down on the floor on his side, curling up to protect himself from the cold on a lovely warm day.

Regret swallowed him and, staring at the watch, he whispered. "I'm sorry, Elizabeth. I let you down."

Unable to bear the world around him any longer, he closed his eyes and silently wept until he fell into an uneasy sleep.

* * *

The swirling cloud of dust and gas began to collapse in on itself. She watched as the collapse released energy and heated up. The area at the centre grew hotter and finally exploded in awe-inspiring fiery light. It was a truly wondrous sight.

She looked over at the ghostly human form of her companion. "Thank you for showing me this."

"It's all right," said Janus, his voice as gentle as ever.

Elizabeth had seen so much since her Ascension. She didn't regret her decision. But to be able to watch events that took place in the Universe? That was incredible. And here she was, watching the birth of a star. What had she done to be worthy of such an honour?

Suddenly, she felt like she was falling. Not falling, crashing. She was in pain, horrible pain. She was lost and alone and… anguished.

No, it wasn't her. Not her, but John. He was suffering some sort of terrible ordeal.

"What is it?" asked Janus.

His voice brought her back somewhat. "I need to go," she said and closed her eyes in preparation.

Janus seemed to know without her saying anymore. "The others won't be happy."

Elizabeth turned her attention to him. "I know. I'm sorry but… I need to see that he's all right."

Janus watched her sternly.

"Please, Janus, just let me go," she implored. "I'll come back, I promise."

Janus sighed. "I would never stop you," he said kindly. "But don't take too long."

She smiled grimly. "Thank you." She returned to her task, focusing her thoughts, finding her way to the man she still loved.


End file.
